diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 907cd28dc28d..efc08e8cf7a5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: - id: renovate-config-validator # use ruff for python files - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.3 + rev: v0.6.4 hooks: - id: ruff files: \.py$ diff --git a/modules/environment-schema.json b/modules/environment-schema.json index b246706e422f..f8107cf09969 100644 --- a/modules/environment-schema.json +++ b/modules/environment-schema.json @@ -10,14 +10,9 @@ }, "channels": { "type": "array", - "items": [ - { - "enum": ["conda-forge"] - }, - { - "enum": ["bioconda"] - } - ], + "items": { + "enum": ["bioconda", "conda-forge"] + }, "minItems": 2 }, "dependencies": { diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml index 51f1fb751b85..71e39be309a8 100644 --- a/modules/nf-core/bcftools/merge/environment.yml +++ b/modules/nf-core/bcftools/merge/environment.yml @@ -2,6 +2,5 @@ name: bcftools_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 41dc1a0d5b46..facb14ea1316 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -11,19 +11,21 @@ process BCFTOOLS_MERGE { tuple val(meta), path(vcfs), path(tbis) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) - path(bed) + tuple val(meta4), path(bed) output: - tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: merged_variants + tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf + tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs def regions = bed ? "--regions-file $bed" : "" def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : @@ -37,7 +39,7 @@ process BCFTOOLS_MERGE { $regions \\ --threads $task.cpus \\ --output ${prefix}.${extension} \\ - $vcfs + $input cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -53,8 +55,16 @@ process BCFTOOLS_MERGE { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml index 877071401920..2caf644e3a39 100644 --- a/modules/nf-core/bcftools/merge/meta.yml +++ b/modules/nf-core/bcftools/merge/meta.yml @@ -46,6 +46,11 @@ input: type: file description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)" pattern: "*.fai" + - meta4: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'genome' ] - bed: type: file description: "(Optional) The bed regions to merge on" @@ -56,22 +61,14 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - vcf_gz: - type: file - description: VCF merged output file (bgzipped) => when `--output-type z` is used - pattern: "*.vcf.gz" - vcf: type: file - description: VCF merged output file => when `--output-type v` is used - pattern: "*.vcf" - - bcf_gz: - type: file - description: BCF merged output file (bgzipped) => when `--output-type b` is used - pattern: "*.bcf.gz" - - bcf: + description: merged output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - index: type: file - description: BCF merged output file => when `--output-type u` is used - pattern: "*.bcf" + description: index of merged output + pattern: "*.{csi,tbi}" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/bcftools/merge/tests/bcf.config b/modules/nf-core/bcftools/merge/tests/bcf.config new file mode 100644 index 000000000000..4467d07d96a0 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/bcf.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type u --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/bcf_gz.config b/modules/nf-core/bcftools/merge/tests/bcf_gz.config new file mode 100644 index 000000000000..280de8db094e --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/bcf_gz.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type b --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test b/modules/nf-core/bcftools/merge/tests/main.nf.test new file mode 100644 index 000000000000..3995fc1a91bb --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test @@ -0,0 +1,853 @@ +nextflow_process { + + name "Test Process BCFTOOLS_MERGE" + script "../main.nf" + process "BCFTOOLS_MERGE" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/merge" + + test("sarscov2 - [vcf, tbi], [], [], []") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf output") { + + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output") { + + config "./vcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf output") { + + config "./bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf") }, + { assert snapshot( + file(process.out.vcf.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output") { + + config "./bcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf.gz") }, + { assert snapshot( + file(process.out.vcf.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.index.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index") { + + config "./vcf_gz_index_csi.config" + + when { + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.index.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("tbi") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.index.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], bed") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + + test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output") { + + config "./nextflow.gvcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ] + input[2] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + ] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - one sample") { + + config "./nextflow.config" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf output - stub") { + + options "-stub" + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - stub") { + + options "-stub" + config "./vcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf output - stub") { + + options "-stub" + config "./bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output - stub") { + + options "-stub" + config "./bcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf.gz") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index - stub") { + + options "-stub" + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub") { + + options "-stub" + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index - stub") { + + options "-stub" + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("tbi") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], bed - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub") { + + options "-stub" + config "./nextflow.gvcf.config" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ] + input[2] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + ] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - 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[vcf, tbi], [], [], [] - one sample - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ], + "index": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T15:13:18.708495878" + }, + "homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ], + "index": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T13:56:45.706125286" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index": { + "content": [ + "e0de448dc8e712956a03ce68d79a0b3a", + "test.vcf.gz.csi", + [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-05T12:33:43.639646108" + }, + "homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output": { + "content": [ + "645b7f7f9131bfe350a9ec3cf82c17fe", + [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T13:55:44.299812124" + }, + "sarscov2 - [vcf, tbi], [], [], [] - one sample": { + "content": [ + "2a374cf02f0c32cf607646167e7f153b", + [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T15:37:38.491844702" + }, + "sarscov2 - [vcf, tbi], [], [], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ], + "index": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T13:17:28.188178904" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ], + "index": [ + [ + { + "id": "test" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T13:18:06.430943593" + }, + "sarscov2 - [vcf, tbi], [], [], []": { + "content": [ + "e0de448dc8e712956a03ce68d79a0b3a", + [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-05T12:31:03.893007442" + }, + "sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output": { + "content": [ + "test.bcf.gz", + [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-05T11:56:56.416361069" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.config b/modules/nf-core/bcftools/merge/tests/nextflow.config new file mode 100644 index 000000000000..c3f0b7159956 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BCFTOOLS_MERGE { + ext.args = '--force-samples --force-single --no-version' + } +} diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config b/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config new file mode 100644 index 000000000000..8c457b716dbe --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config @@ -0,0 +1,5 @@ +process { + withName: BCFTOOLS_MERGE { + ext.args = { "--force-samples --no-version --output-type z --gvcf $fasta" } + } +} diff --git a/modules/nf-core/bcftools/merge/tests/tags.yml b/modules/nf-core/bcftools/merge/tests/tags.yml new file mode 100644 index 000000000000..1464d0c1c309 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/merge: + - "modules/nf-core/bcftools/merge/**" diff --git a/modules/nf-core/bcftools/merge/tests/vcf.config b/modules/nf-core/bcftools/merge/tests/vcf.config new file mode 100644 index 000000000000..759222e58ca7 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type v --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz.config b/modules/nf-core/bcftools/merge/tests/vcf_gz.config new file mode 100644 index 000000000000..8b6ad8b4fdcf --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type z --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config new file mode 100644 index 000000000000..9f1e9b1d8f2b --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config new file mode 100644 index 000000000000..8308ee1aed4f --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config new file mode 100644 index 000000000000..9be4075bc17b --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/biobambam/bamsormadup/main.nf b/modules/nf-core/biobambam/bamsormadup/main.nf index dc25a3fae408..10bb1a7f2e81 100644 --- a/modules/nf-core/biobambam/bamsormadup/main.nf +++ b/modules/nf-core/biobambam/bamsormadup/main.nf @@ -48,4 +48,22 @@ process BIOBAMBAM_BAMSORMADUP { bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' ) END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = args.contains("outputformat=cram") ? "cram" : "bam" + if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output." + + """ + touch ${prefix}.${suffix} + touch ${prefix}.metrics.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bamcat: \$(echo \$(bamcat --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' ) + bamcollate2: \$(echo \$(bamcollate2 --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' ) + bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test b/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test new file mode 100644 index 000000000000..43272ff16046 --- /dev/null +++ b/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test @@ -0,0 +1,105 @@ + +nextflow_process { + + name "Test Process BIOBAMBAM_BAMSORMADUP" + script "../main.nf" + process "BIOBAMBAM_BAMSORMADUP" + + tag "modules" + tag "modules_nfcore" + tag "biobambam" + tag "biobambam/bamsormadup" + + test("test-biobambam-bamsormadup-multi-input") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + ] + input[1] = [[:],[]] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.bam_index, + process.out.cram, + file(process.out.metrics[0][1]).readLines()[3..5], + process.out.versions + ).match() + } + ) + } + } + + test("test-biobambam-bamsormadup-single-input") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + ] + input[1] = [[:],[]] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.bam_index, + process.out.cram, + file(process.out.metrics[0][1]).readLines()[3..5], + process.out.versions + ).match() + } + ) + } + } + + test("test-biobambam-bamsormadup-single-input-stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + ] + input[1] = [[:],[]] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test.snap b/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test.snap new file mode 100644 index 000000000000..f7a41ca6fff1 --- /dev/null +++ b/modules/nf-core/biobambam/bamsormadup/tests/main.nf.test.snap @@ -0,0 +1,115 @@ +{ + "test-biobambam-bamsormadup-single-input": { + "content": [ + "e296148e4f68882cc91fb624e392f539", + [ + + ], + [ + + ], + [ + "LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE", + "lib1\t3\t97\t3\t0\t0\t0\t0\t-1", + "" + ], + [ + "versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:00:39.772883" + }, + "test-biobambam-bamsormadup-multi-input": { + "content": [ + "3dc03384b330e3f16e15691c9189e890", + [ + + ], + [ + + ], + [ + "LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE", + "lib1\t3\t97\t3\t0\t0\t0\t0\t-1", + "testN\t0\t2820\t2\t0\t828\t0\t0.293617\t3807" + ], + [ + "versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:00:31.187999" + }, + "test-biobambam-bamsormadup-single-input-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_index": [ + + ], + "cram": [ + + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:57:13.430982" + } +} \ No newline at end of file diff --git a/modules/nf-core/circexplorer2/parse/environment.yml b/modules/nf-core/circexplorer2/parse/environment.yml index 52e172e7edd1..17613a2a1914 100644 --- a/modules/nf-core/circexplorer2/parse/environment.yml +++ b/modules/nf-core/circexplorer2/parse/environment.yml @@ -2,6 +2,5 @@ name: circexplorer2_parse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::circexplorer2=2.3.8 diff --git a/modules/nf-core/circexplorer2/parse/meta.yml b/modules/nf-core/circexplorer2/parse/meta.yml index ef3ebf856437..83e6e9d35b4e 100644 --- a/modules/nf-core/circexplorer2/parse/meta.yml +++ b/modules/nf-core/circexplorer2/parse/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://github.com/YangLab/CIRCexplorer2/" documentation: "https://circexplorer2.readthedocs.io/en/latest/" doi: "10.1101/gr.202895.115" - licence: "['MIT License']" + licence: ["MIT License"] input: - meta: type: map diff --git a/modules/nf-core/circexplorer2/parse/tests/main.nf.test b/modules/nf-core/circexplorer2/parse/tests/main.nf.test new file mode 100644 index 000000000000..4768ab5ddbce --- /dev/null +++ b/modules/nf-core/circexplorer2/parse/tests/main.nf.test @@ -0,0 +1,62 @@ + +nextflow_process { + + name "Test Process CIRCEXPLORER2_PARSE" + script "../main.nf" + process "CIRCEXPLORER2_PARSE" + + tag "modules" + tag "modules_nfcore" + tag "circexplorer2" + tag "circexplorer2/parse" + + test("test-circexplorer2-parse") { + + when { + process { + """ + input[0] = [ + [ id:'fust1_3' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction") + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.junction[0][1]).text.contains('FUSIONJUNC') }, + { assert snapshot( + file(process.out.junction[0][1]).name, // unstable + process.out.versions + ).match() + } + ) + } + } + + test("test-circexplorer2-parse-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'fust1_3' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction") + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/circexplorer2/parse/tests/main.nf.test.snap b/modules/nf-core/circexplorer2/parse/tests/main.nf.test.snap new file mode 100644 index 000000000000..f9b6869f7719 --- /dev/null +++ b/modules/nf-core/circexplorer2/parse/tests/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "test-circexplorer2-parse-stub": { + "content": [ + { + "0": [ + [ + { + "id": "fust1_3" + }, + "fust1_3.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,6490a204cc08154871418e5fbb3aff17" + ], + "junction": [ + [ + { + "id": "fust1_3" + }, + "fust1_3.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,6490a204cc08154871418e5fbb3aff17" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:58:38.034614" + }, + "test-circexplorer2-parse": { + "content": [ + "fust1_3.bed", + [ + "versions.yml:md5,6490a204cc08154871418e5fbb3aff17" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:53:55.470118" + } +} \ No newline at end of file diff --git a/modules/nf-core/cnvkit/call/environment.yml b/modules/nf-core/cnvkit/call/environment.yml index 3b96de7008ff..4aaf29c04f0e 100644 --- a/modules/nf-core/cnvkit/call/environment.yml +++ b/modules/nf-core/cnvkit/call/environment.yml @@ -2,6 +2,5 @@ name: cnvkit_call channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvkit=0.9.10 diff --git a/modules/nf-core/cnvkit/call/main.nf b/modules/nf-core/cnvkit/call/main.nf index fade6df0fd1e..06d51e857ecd 100644 --- a/modules/nf-core/cnvkit/call/main.nf +++ b/modules/nf-core/cnvkit/call/main.nf @@ -33,4 +33,15 @@ process CNVKIT_CALL { cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.cns + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g') + END_VERSIONS + """ } diff --git a/modules/nf-core/cnvkit/call/tests/main.nf.test b/modules/nf-core/cnvkit/call/tests/main.nf.test new file mode 100644 index 000000000000..6012ef137f71 --- /dev/null +++ b/modules/nf-core/cnvkit/call/tests/main.nf.test @@ -0,0 +1,83 @@ + +nextflow_process { + + name "Test Process CNVKIT_CALL" + script "../main.nf" + process "CNVKIT_CALL" + + tag "modules" + tag "modules_nfcore" + tag "cnvkit" + tag "cnvkit/call" + + test("test-cnvkit-call") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true), + [] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-cnvkit-call-with-vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-cnvkit-call-with-vcf-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/cnvkit/call/tests/main.nf.test.snap b/modules/nf-core/cnvkit/call/tests/main.nf.test.snap new file mode 100644 index 000000000000..844a415ecf6b --- /dev/null +++ b/modules/nf-core/cnvkit/call/tests/main.nf.test.snap @@ -0,0 +1,107 @@ +{ + "test-cnvkit-call": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,7746029caf9ecc134a075a2d50be269f" + ] + ], + "1": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ], + "cns": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,7746029caf9ecc134a075a2d50be269f" + ] + ], + "versions": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:24:41.048386" + }, + "test-cnvkit-call-with-vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,2a4b3da8a8131a4ed4ae902a9f96a405" + ] + ], + "1": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ], + "cns": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,2a4b3da8a8131a4ed4ae902a9f96a405" + ] + ], + "versions": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:24:50.134984" + }, + "test-cnvkit-call-with-vcf-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ], + "cns": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:24:56.743954" + } +} \ No newline at end of file diff --git a/modules/nf-core/emboss/revseq/environment.yml b/modules/nf-core/emboss/revseq/environment.yml index cc8acbdfe674..5e2d20e5b7cf 100644 --- a/modules/nf-core/emboss/revseq/environment.yml +++ b/modules/nf-core/emboss/revseq/environment.yml @@ -2,6 +2,5 @@ name: emboss_revseq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::emboss=6.6.0 diff --git a/modules/nf-core/emboss/revseq/tests/main.nf.test b/modules/nf-core/emboss/revseq/tests/main.nf.test new file mode 100644 index 000000000000..b8f980ea6db2 --- /dev/null +++ b/modules/nf-core/emboss/revseq/tests/main.nf.test @@ -0,0 +1,57 @@ + +nextflow_process { + + name "Test Process EMBOSS_REVSEQ" + script "../main.nf" + process "EMBOSS_REVSEQ" + + tag "modules" + tag "modules_nfcore" + tag "emboss" + tag "emboss/revseq" + + test("test-emboss-revseq") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-emboss-revseq-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/emboss/revseq/tests/main.nf.test.snap b/modules/nf-core/emboss/revseq/tests/main.nf.test.snap new file mode 100644 index 000000000000..cf064fbebb51 --- /dev/null +++ b/modules/nf-core/emboss/revseq/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-emboss-revseq-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rev.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,6036bdf4f510114f18e8304e88b7c453" + ], + "revseq": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rev.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,6036bdf4f510114f18e8304e88b7c453" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:23:57.293555" + }, + "test-emboss-revseq": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rev.fasta:md5,78a4b77f08b5c95ab24e592f543f679c" + ] + ], + "1": [ + "versions.yml:md5,6036bdf4f510114f18e8304e88b7c453" + ], + "revseq": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rev.fasta:md5,78a4b77f08b5c95ab24e592f543f679c" + ] + ], + "versions": [ + "versions.yml:md5,6036bdf4f510114f18e8304e88b7c453" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:23:52.761673" + } +} \ No newline at end of file diff --git a/modules/nf-core/geoquery/getgeo/environment.yml b/modules/nf-core/geoquery/getgeo/environment.yml index bfbf8a2df29b..3385fdc5e478 100644 --- a/modules/nf-core/geoquery/getgeo/environment.yml +++ b/modules/nf-core/geoquery/getgeo/environment.yml @@ -2,6 +2,6 @@ name: geoquery_getgeo channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::bioconductor-geoquery=2.66.0 + - bioconda::bioconductor-geoquery=2.70.0 + - conda-forge::r-base=4.3.2 # Locked with container diff --git a/modules/nf-core/geoquery/getgeo/main.nf b/modules/nf-core/geoquery/getgeo/main.nf index c66aca93ff76..ec32b43d5cf2 100644 --- a/modules/nf-core/geoquery/getgeo/main.nf +++ b/modules/nf-core/geoquery/getgeo/main.nf @@ -4,8 +4,8 @@ process GEOQUERY_GETGEO { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-geoquery:2.66.0--r42hdfd78af_0' : - 'biocontainers/bioconductor-geoquery:2.66.0--r42hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-geoquery:2.70.0--r43hdfd78af_0' : + 'biocontainers/bioconductor-geoquery:2.70.0--r43hdfd78af_0' }" input: tuple val(meta), val(querygse) @@ -21,4 +21,18 @@ process GEOQUERY_GETGEO { script: template 'getgeo.R' + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.rds + touch ${prefix}.matrix.tsv + touch ${prefix}.annotation.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + r-base: \$(Rscript -e 'R.Version()\$version.string' | sed -n 's|\\[1\\] "R version \\(.*\\) (.*|\\1|p') + bioconductor-geoquery: \$(Rscript -e 'packageVersion("GEOquery")' | sed -n 's|\\[1\\] ‘\\(.*\\)’|\\1|p') + END_VERSIONS + """ } diff --git a/modules/nf-core/geoquery/getgeo/meta.yml b/modules/nf-core/geoquery/getgeo/meta.yml index ca0074c7a533..b8000288415f 100644 --- a/modules/nf-core/geoquery/getgeo/meta.yml +++ b/modules/nf-core/geoquery/getgeo/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html" tool_dev_url: "https://github.com/seandavi/GEOquery" doi: "10.1093/bioinformatics/btm254" - licence: "MIT" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/geoquery/getgeo/tests/main.nf.test b/modules/nf-core/geoquery/getgeo/tests/main.nf.test new file mode 100644 index 000000000000..7debd2c0b12c --- /dev/null +++ b/modules/nf-core/geoquery/getgeo/tests/main.nf.test @@ -0,0 +1,94 @@ + +nextflow_process { + + name "Test Process GEOQUERY_GETGEO" + script "../main.nf" + process "GEOQUERY_GETGEO" + + tag "modules" + tag "modules_nfcore" + tag "geoquery" + tag "geoquery/getgeo" + + test("test-geoquery-getgeo") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + 'GSE50790' + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.rds[0][1]).name, + file(process.out.expression[0][1]).name, // unstable + process.out.annotation, + process.out.versions, + file(process.out.versions[0]).readLines().collect { it.trim() } // Trap to catch conda version mismatches + ).match() + } + ) + } + } + + test("test-geoquery-getgeo-with-metacols") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + 'GSE50790' + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.rds[0][1]).name, + file(process.out.expression[0][1]).name, // unstable + process.out.annotation, + process.out.versions + ).match() + } + ) + } + } + + test("test-geoquery-getgeo-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + 'GSE50790' + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/geoquery/getgeo/tests/main.nf.test.snap b/modules/nf-core/geoquery/getgeo/tests/main.nf.test.snap new file mode 100644 index 000000000000..c80986d960f2 --- /dev/null +++ b/modules/nf-core/geoquery/getgeo/tests/main.nf.test.snap @@ -0,0 +1,116 @@ +{ + "test-geoquery-getgeo-with-metacols": { + "content": [ + "test.eset.rds", + "test.matrix.tsv", + [ + [ + { + "id": "test" + }, + "test.annotation.tsv:md5,40300ae222ae35fa54daf10a1b86e830" + ] + ], + [ + "versions.yml:md5,6364f5393cdbde3b4c7c92aac6f70dd0" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:41:39.616967" + }, + "test-geoquery-getgeo-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.rds:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.matrix.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.annotation.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,6364f5393cdbde3b4c7c92aac6f70dd0" + ], + "annotation": [ + [ + { + "id": "test" + }, + "test.annotation.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "expression": [ + [ + { + "id": "test" + }, + "test.matrix.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "rds": [ + [ + { + "id": "test" + }, + "test.rds:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,6364f5393cdbde3b4c7c92aac6f70dd0" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:50:33.782155" + }, + "test-geoquery-getgeo": { + "content": [ + "eset.rds", + "matrix.tsv", + [ + [ + { + "id": "test" + }, + "annotation.tsv:md5,4dbb874b49a11dff13557f58da643ee0" + ] + ], + [ + "versions.yml:md5,6364f5393cdbde3b4c7c92aac6f70dd0" + ], + [ + "\"GEOQUERY_GETGEO\":", + "r-base: 4.3.2", + "bioconductor-geoquery: 2.70.0" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:41:16.597153" + } +} \ No newline at end of file diff --git a/modules/nf-core/geoquery/getgeo/tests/nextflow.config b/modules/nf-core/geoquery/getgeo/tests/nextflow.config new file mode 100644 index 000000000000..9b3028d7bbd7 --- /dev/null +++ b/modules/nf-core/geoquery/getgeo/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: 'GEOQUERY_GETGEO' { + ext.args = { "--metacols \"ID,ENTREZ_GENE_ID,Gene Symbol,Sequence Type\"" } + ext.prefix = { "${meta.id}." } + } +} diff --git a/modules/nf-core/gfaffix/environment.yml b/modules/nf-core/gfaffix/environment.yml index 09e63d2483eb..77262a47394c 100644 --- a/modules/nf-core/gfaffix/environment.yml +++ b/modules/nf-core/gfaffix/environment.yml @@ -2,6 +2,5 @@ name: gfaffix channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gfaffix=0.1.5 + - bioconda::gfaffix=0.1.5b diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index efbfe28ffa19..2abdd634a59a 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -30,7 +30,19 @@ process GFAFFIX { cat <<-END_VERSIONS > versions.yml "${task.process}": - gfaffix: \$(gfaffix --version 2>&1 | grep -o 'gfaffix .*' | cut -f2 -d ' ') + gfaffix: \$(gfaffix --version | grep -o 'gfaffix .*' | cut -f2 -d ' ') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.gfaffix.gfa + touch ${prefix}.affixes.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gfaffix: \$(gfaffix --version | grep -o 'gfaffix .*' | cut -f2 -d ' ') END_VERSIONS """ } diff --git a/modules/nf-core/gfaffix/tests/main.nf.test b/modules/nf-core/gfaffix/tests/main.nf.test new file mode 100644 index 000000000000..41fca58b64e7 --- /dev/null +++ b/modules/nf-core/gfaffix/tests/main.nf.test @@ -0,0 +1,63 @@ + +nextflow_process { + + name "Test Process GFAFFIX" + script "../main.nf" + process "GFAFFIX" + + tag "modules" + tag "modules_nfcore" + tag "gfaffix" + + test("test-gfaffix") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.gfa, + process.out.affixes, + process.out.versions, + file(process.out.versions[0]).readLines().collect { it.trim() }, // Trap for conda version mismatches + ).match() + } + ) + } + } + + test("test-gfaffix-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gfaffix/tests/main.nf.test.snap b/modules/nf-core/gfaffix/tests/main.nf.test.snap new file mode 100644 index 000000000000..6ff3e8df4387 --- /dev/null +++ b/modules/nf-core/gfaffix/tests/main.nf.test.snap @@ -0,0 +1,83 @@ +{ + "test-gfaffix": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.gfaffix.gfa:md5,30d7a68fc07623779dbb3d708320c844" + ] + ], + [ + [ + { + "id": "test" + }, + "test.affixes.txt:md5,c3540baa386462552d7ebe4e4b7eda6a" + ] + ], + [ + "versions.yml:md5,3ec7c6a9cbafbb8131f4e325e140aa80" + ], + [ + "\"GFAFFIX\":", + "gfaffix: 0.1.5b" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:14:01.340269" + }, + "test-gfaffix-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.gfaffix.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.affixes.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,3ec7c6a9cbafbb8131f4e325e140aa80" + ], + "affixes": [ + [ + { + "id": "test" + }, + "test.affixes.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gfa": [ + [ + { + "id": "test" + }, + "test.gfaffix.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3ec7c6a9cbafbb8131f4e325e140aa80" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:36:34.068923" + } +} \ No newline at end of file diff --git a/modules/nf-core/goleft/indexsplit/environment.yml b/modules/nf-core/goleft/indexsplit/environment.yml index d8c37692adc2..192482ae4576 100644 --- a/modules/nf-core/goleft/indexsplit/environment.yml +++ b/modules/nf-core/goleft/indexsplit/environment.yml @@ -2,6 +2,5 @@ name: goleft_indexsplit channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::goleft=0.2.4 diff --git a/modules/nf-core/goleft/indexsplit/meta.yml b/modules/nf-core/goleft/indexsplit/meta.yml index 023a25a4ce3c..49ee3b4f4ebd 100644 --- a/modules/nf-core/goleft/indexsplit/meta.yml +++ b/modules/nf-core/goleft/indexsplit/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/brentp/goleft" tool_dev_url: "https://github.com/brentp/goleft" doi: "10.1093/gigascience/gix090" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/goleft/indexsplit/tests/main.nf.test b/modules/nf-core/goleft/indexsplit/tests/main.nf.test new file mode 100644 index 000000000000..9469e402f78d --- /dev/null +++ b/modules/nf-core/goleft/indexsplit/tests/main.nf.test @@ -0,0 +1,68 @@ + +nextflow_process { + + name "Test Process GOLEFT_INDEXSPLIT" + script "../main.nf" + process "GOLEFT_INDEXSPLIT" + + tag "modules" + tag "modules_nfcore" + tag "goleft" + tag "goleft/indexsplit" + + test("test-goleft-indexsplit") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'sarscov2'], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + + ] + input[2] = 10 + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-goleft-indexsplit-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'sarscov2'], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[2] = 10 + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/goleft/indexsplit/tests/main.nf.test.snap b/modules/nf-core/goleft/indexsplit/tests/main.nf.test.snap new file mode 100644 index 000000000000..d8c7963eb10c --- /dev/null +++ b/modules/nf-core/goleft/indexsplit/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-goleft-indexsplit": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,6158ae22773bda2b1380c1f7e324d7a9" + ] + ], + "1": [ + "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,6158ae22773bda2b1380c1f7e324d7a9" + ] + ], + "versions": [ + "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T08:39:21.842028" + }, + "test-goleft-indexsplit-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T08:39:26.342137" + } +} \ No newline at end of file diff --git a/modules/nf-core/graphtyper/vcfconcatenate/environment.yml b/modules/nf-core/graphtyper/vcfconcatenate/environment.yml index 0bba162dfadb..0f22a4f9d518 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/environment.yml +++ b/modules/nf-core/graphtyper/vcfconcatenate/environment.yml @@ -2,6 +2,5 @@ name: graphtyper_vcfconcatenate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::graphtyper=2.7.2 diff --git a/modules/nf-core/graphtyper/vcfconcatenate/main.nf b/modules/nf-core/graphtyper/vcfconcatenate/main.nf index efd0dbbf2d35..cf0ae5dbc31f 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/main.nf +++ b/modules/nf-core/graphtyper/vcfconcatenate/main.nf @@ -36,4 +36,19 @@ process GRAPHTYPER_VCFCONCATENATE { graphtyper: \$(graphtyper --help | tail -n 1 | sed 's/^ //') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$vcf" == "${prefix}.vcf.gz") { + error "Input and output names are the same, set prefix in module configuration to disambiguate!" + } + """ + echo | gzip > ${prefix}.vcf.gz + touch ${prefix}.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + graphtyper: \$(graphtyper --help | tail -n 1 | sed 's/^ //') + END_VERSIONS + """ } diff --git a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml index 92ec7981fddf..a34a83e83fc3 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml +++ b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide" tool_dev_url: "https://github.com/DecodeGenetics/graphtyper" doi: "10.1038/ng.3964" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test new file mode 100644 index 000000000000..a596539386b6 --- /dev/null +++ b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test @@ -0,0 +1,70 @@ + +nextflow_process { + + name "Test Process GRAPHTYPER_VCFCONCATENATE" + script "../main.nf" + process "GRAPHTYPER_VCFCONCATENATE" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "graphtyper" + tag "graphtyper/vcfconcatenate" + + test("test-graphtyper-vcfconcatenate") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-graphtyper-vcfconcatenate-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test.snap b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test.snap new file mode 100644 index 000000000000..ab8947ec4adb --- /dev/null +++ b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test.snap @@ -0,0 +1,69 @@ +{ + "test-graphtyper-vcfconcatenate-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "prefix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "prefix.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,da65963fb13e605b770c500fcddca43f" + ], + "tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "prefix.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "prefix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,da65963fb13e605b770c500fcddca43f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T08:42:58.201156" + }, + "test-graphtyper-vcfconcatenate": { + "content": [ + "ff00185efbeeac85dbe22d3b63466f71", + "prefix.vcf.gz.tbi", + [ + "versions.yml:md5,da65963fb13e605b770c500fcddca43f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T08:42:53.20738" + } +} \ No newline at end of file diff --git a/modules/nf-core/graphtyper/vcfconcatenate/tests/nextflow.config b/modules/nf-core/graphtyper/vcfconcatenate/tests/nextflow.config new file mode 100644 index 000000000000..31dce6d2949e --- /dev/null +++ b/modules/nf-core/graphtyper/vcfconcatenate/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GRAPHTYPER_VCFCONCATENATE { + ext.prefix = "prefix" + } +} diff --git a/modules/nf-core/gubbins/environment.yml b/modules/nf-core/gubbins/environment.yml index 915378223606..0e8285b41c2d 100644 --- a/modules/nf-core/gubbins/environment.yml +++ b/modules/nf-core/gubbins/environment.yml @@ -2,6 +2,5 @@ name: gubbins channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gubbins=3.0.0 + - bioconda::gubbins=3.3.5 diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index a934f1dd629e..2d91dfc0009a 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -3,8 +3,8 @@ process GUBBINS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0' : - 'biocontainers/gubbins:3.0.0--py39h5bf99c6_0' }" + 'https://depot.galaxyproject.org/singularity/gubbins:3.3.5--py39pl5321he4a0461_0' : + 'biocontainers/gubbins:3.3.5--py39pl5321he4a0461_0' }" input: path alignment @@ -27,6 +27,9 @@ process GUBBINS { script: def args = task.ext.args ?: '' """ + mkdir numba_cache_dir + export NUMBA_CACHE_DIR='./numba_cache_dir' + run_gubbins.py \\ --threads $task.cpus \\ $args \\ @@ -36,4 +39,26 @@ process GUBBINS { gubbins: \$(run_gubbins.py --version 2>&1) END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + """ + mkdir numba_cache_dir + export NUMBA_CACHE_DIR='./numba_cache_dir' + + touch ${alignment.baseName}.fasta + touch ${alignment.baseName}.gff + touch ${alignment.baseName}.vcf + touch ${alignment.baseName}.csv + touch ${alignment.baseName}.phylip + touch ${alignment.baseName}.recombination_predictions.embl + touch ${alignment.baseName}.branch_base_reconstruction.embl + touch ${alignment.baseName}.final_tree.tre + touch ${alignment.baseName}.node_labelled.final_tree.tre + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gubbins: \$(run_gubbins.py --version 2>&1) + END_VERSIONS + """ } diff --git a/modules/nf-core/gubbins/meta.yml b/modules/nf-core/gubbins/meta.yml index 30f6bd7f4327..191660b82ae8 100644 --- a/modules/nf-core/gubbins/meta.yml +++ b/modules/nf-core/gubbins/meta.yml @@ -4,6 +4,7 @@ licence: ["GPL-2.0-only"] keywords: - recombination - alignment + - phylogeny tools: - gubbins: description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. diff --git a/modules/nf-core/gubbins/tests/main.nf.test b/modules/nf-core/gubbins/tests/main.nf.test new file mode 100644 index 000000000000..357d3d71d063 --- /dev/null +++ b/modules/nf-core/gubbins/tests/main.nf.test @@ -0,0 +1,63 @@ + +nextflow_process { + + name "Test Process GUBBINS" + script "../main.nf" + process "GUBBINS" + + tag "modules" + tag "modules_nfcore" + tag "gubbins" + + test("sarscov2-alignment") { + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fasta, + process.out.gff, + path(process.out.vcf[0]).vcf.variantsMD5, + process.out.stats, + process.out.phylip, + file(process.out.embl_predicted[0]).name, // empty + process.out.embl_branch, + process.out.tree[0].collect { file(it).name }, // unstable + file(process.out.tree_labelled[0]).name, // unstable + process.out.versions + ).match() + } + ) + } + } + + test("sarscov2-alignment-stub") { + options '-stub' + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gubbins/tests/main.nf.test.snap b/modules/nf-core/gubbins/tests/main.nf.test.snap new file mode 100644 index 000000000000..33f66d8c9416 --- /dev/null +++ b/modules/nf-core/gubbins/tests/main.nf.test.snap @@ -0,0 +1,113 @@ +{ + "sarscov2-alignment-stub": { + "content": [ + { + "0": [ + "all_sites.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + "all_sites.gff:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "2": [ + "all_sites.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "3": [ + "all_sites.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "4": [ + "all_sites.phylip:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "5": [ + "all_sites.recombination_predictions.embl:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "6": [ + "all_sites.branch_base_reconstruction.embl:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "7": [ + [ + "all_sites.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e", + "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "9": [ + "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76" + ], + "embl_branch": [ + "all_sites.branch_base_reconstruction.embl:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "embl_predicted": [ + "all_sites.recombination_predictions.embl:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "fasta": [ + "all_sites.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "gff": [ + "all_sites.gff:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "phylip": [ + "all_sites.phylip:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "stats": [ + "all_sites.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "tree": [ + [ + "all_sites.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e", + "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tree_labelled": [ + "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "vcf": [ + "all_sites.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:20:39.212181" + }, + "sarscov2-alignment": { + "content": [ + [ + "all_sites.filtered_polymorphic_sites.fasta:md5,0f945512f071fd1599bb7455492e31bc" + ], + [ + "all_sites.recombination_predictions.gff:md5,7605a21ad8812866adbdb5cada8a59d4" + ], + "d314daa06c635c0b31b132a1092ee4e3", + [ + "all_sites.per_branch_statistics.csv:md5,8012a76a2486a8b3dfe78d6902b56ed4" + ], + [ + "all_sites.filtered_polymorphic_sites.phylip:md5,d28da2dd14d08bbb996756064516aee1" + ], + "all_sites.recombination_predictions.embl", + [ + "all_sites.branch_base_reconstruction.embl:md5,9dfd7e411404360ce4a7938aab8db701" + ], + [ + "all_sites.final_tree.tre", + "all_sites.node_labelled.final_tree.tre" + ], + "all_sites.node_labelled.final_tree.tre", + [ + "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:16:35.669362" + } +} \ No newline at end of file diff --git a/modules/nf-core/hapibd/environment.yml b/modules/nf-core/hapibd/environment.yml index 2902e831e196..4c2f52d3d384 100644 --- a/modules/nf-core/hapibd/environment.yml +++ b/modules/nf-core/hapibd/environment.yml @@ -2,6 +2,5 @@ name: hapibd channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hap-ibd=1.0.rev20May22.818 diff --git a/modules/nf-core/hapibd/main.nf b/modules/nf-core/hapibd/main.nf index cd920ca29a18..92c355b65e74 100644 --- a/modules/nf-core/hapibd/main.nf +++ b/modules/nf-core/hapibd/main.nf @@ -47,4 +47,25 @@ process HAPIBD { hapibd: \$(hap-ibd 2>&1 |head -n1 | sed 's/^hap-ibd.jar \\[ version //; s/, /rev/; s/ \\]//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + def avail_mem = 3072 + if (!task.memory) { + log.info '[hapibd] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = (task.memory.mega*0.8).intValue() + } + + """ + touch ${prefix}.log + echo | gzip > ${prefix}.hbd.gz + echo | gzip > ${prefix}.ibd.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hapibd: \$(hap-ibd 2>&1 |head -n1 | sed 's/^hap-ibd.jar \\[ version //; s/, /rev/; s/ \\]//') + END_VERSIONS + """ } diff --git a/modules/nf-core/hapibd/meta.yml b/modules/nf-core/hapibd/meta.yml index 686ae88bf22d..8def0c8d6625 100644 --- a/modules/nf-core/hapibd/meta.yml +++ b/modules/nf-core/hapibd/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://github.com/browning-lab/hap-ibd/blob/master/README.md" documentation: "https://github.com/browning-lab/hap-ibd/blob/master/README.md" doi: "10.1016/j.ajhg.2020.02.010" - licence: "['Apache-2.0']" + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/nf-core/hapibd/tests/main.nf.test b/modules/nf-core/hapibd/tests/main.nf.test new file mode 100644 index 000000000000..85d14460690e --- /dev/null +++ b/modules/nf-core/hapibd/tests/main.nf.test @@ -0,0 +1,99 @@ + +nextflow_process { + + name "Test Process HAPIBD" + script "../main.nf" + process "HAPIBD" + + tag "modules" + tag "modules_nfcore" + tag "hapibd" + + test("test-hapibd") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) + ] + input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) + input[2] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.log[0][1]).text.contains('End Time') }, + { assert snapshot( + file(process.out.hbd[0][1]).name, // empty + file(process.out.ibd[0][1]).name, // unstable + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-hapibd-excludesamples") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) + ] + input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) + input[2] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/excludeSamples.txt", checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.log[0][1]).text.contains('End Time') }, + { assert snapshot( + file(process.out.hbd[0][1]).name, // empty + file(process.out.ibd[0][1]).name, // unstable + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-hapibd-excludesamples-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) + ] + input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) + input[2] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/excludeSamples.txt", checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/hapibd/tests/main.nf.test.snap b/modules/nf-core/hapibd/tests/main.nf.test.snap new file mode 100644 index 000000000000..b5a5951f27f5 --- /dev/null +++ b/modules/nf-core/hapibd/tests/main.nf.test.snap @@ -0,0 +1,103 @@ +{ + "test-hapibd": { + "content": [ + "test.hbd.gz", + "test.ibd.gz", + "test.log", + [ + "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:50:07.8312" + }, + "test-hapibd-excludesamples": { + "content": [ + "test.hbd.gz", + "test.ibd.gz", + "test.log", + [ + "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:50:29.730739" + }, + "test-hapibd-excludesamples-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hbd.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ibd.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a" + ], + "hbd": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hbd.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "ibd": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ibd.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:40:49.71258" + } +} \ No newline at end of file diff --git a/modules/nf-core/haplogrep2/classify/meta.yml b/modules/nf-core/haplogrep2/classify/meta.yml index 8174218eb489..c5399f5c00dd 100644 --- a/modules/nf-core/haplogrep2/classify/meta.yml +++ b/modules/nf-core/haplogrep2/classify/meta.yml @@ -1,14 +1,16 @@ name: "haplogrep2_classify" description: classification into haplogroups keywords: - - haplogroups. + - haplogroups + - classify + - mtDNA tools: - "haplogrep2": description: "A tool for mtDNA haplogroup classification." homepage: "https://github.com/seppinho/haplogrep-cmd" documentation: "https://github.com/seppinho/haplogrep-cmd" tool_dev_url: "https://github.com/seppinho/haplogrep-cmd" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/haplogrep2/classify/tests/main.nf.test b/modules/nf-core/haplogrep2/classify/tests/main.nf.test new file mode 100644 index 000000000000..a5c42b3311b4 --- /dev/null +++ b/modules/nf-core/haplogrep2/classify/tests/main.nf.test @@ -0,0 +1,59 @@ + +nextflow_process { + + name "Test Process HAPLOGREP2_CLASSIFY" + script "../main.nf" + process "HAPLOGREP2_CLASSIFY" + + tag "modules" + tag "modules_nfcore" + tag "haplogrep2" + tag "haplogrep2/classify" + + test("test-haplogrep2-classify") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) + ] + input[1] = 'vcf' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-haplogrep2-classify-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) + ] + input[1] = 'vcf' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/haplogrep2/classify/tests/main.nf.test.snap b/modules/nf-core/haplogrep2/classify/tests/main.nf.test.snap new file mode 100644 index 000000000000..2ea00379fcbd --- /dev/null +++ b/modules/nf-core/haplogrep2/classify/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-haplogrep2-classify": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.txt:md5,cf9a4cf886e75233083313d8758566a0" + ] + ], + "1": [ + "versions.yml:md5,b89c2ae3ff8722a536c4042ed4330f25" + ], + "txt": [ + [ + { + "id": "test", + "single_end": false + }, + "test.txt:md5,cf9a4cf886e75233083313d8758566a0" + ] + ], + "versions": [ + "versions.yml:md5,b89c2ae3ff8722a536c4042ed4330f25" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:15:54.953862" + }, + "test-haplogrep2-classify-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,b89c2ae3ff8722a536c4042ed4330f25" + ], + "txt": [ + [ + { + "id": "test", + "single_end": false + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b89c2ae3ff8722a536c4042ed4330f25" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:12:30.597805" + } +} \ No newline at end of file diff --git a/modules/nf-core/hmmer/hmmbuild/environment.yml b/modules/nf-core/hmmer/hmmbuild/environment.yml index 1957ad5c63aa..5eb083ed9ed9 100644 --- a/modules/nf-core/hmmer/hmmbuild/environment.yml +++ b/modules/nf-core/hmmer/hmmbuild/environment.yml @@ -2,6 +2,5 @@ name: hmmer_hmmbuild channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmer=3.3.2 diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 3e3022fe643a..b4629cb47a65 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -41,4 +41,16 @@ process HMMER_HMMBUILD { hmmer: \$(echo \$(hmmbuild -h | grep HMMER | sed 's/# HMMER //' | sed 's/ .*//' 2>&1)) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo | gzip > ${prefix}.hmm.gz + touch ${prefix}.hmmbuild.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hmmer: \$(echo \$(hmmbuild -h | grep HMMER | sed 's/# HMMER //' | sed 's/ .*//' 2>&1)) + END_VERSIONS + """ } diff --git a/modules/nf-core/hmmer/hmmbuild/meta.yml b/modules/nf-core/hmmer/hmmbuild/meta.yml index 4bf6b1cfee90..fb9d50830016 100644 --- a/modules/nf-core/hmmer/hmmbuild/meta.yml +++ b/modules/nf-core/hmmer/hmmbuild/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "http://hmmer.org/documentation.html" tool_dev_url: "https://github.com/EddyRivasLab/hmmer" doi: "10.1371/journal.pcbi.1002195" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test new file mode 100644 index 000000000000..d7c058255eaa --- /dev/null +++ b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test @@ -0,0 +1,66 @@ + +nextflow_process { + + name "Test Process HMMER_HMMBUILD" + script "../main.nf" + process "HMMER_HMMBUILD" + + tag "modules" + tag "modules_nfcore" + tag "hmmer" + tag "hmmer/hmmbuild" + + test("test-hmmer-hmmbuild") { + + when { + process { + """ + input[0] = [ + [ id: 'PF14720' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) + ] + input[1] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.hmmbuildout[0]).text.contains('CPU time:') }, + { assert snapshot( + file(process.out.hmm[0][1]).name, // unstable + file(process.out.hmmbuildout[0]).name, // unstable + process.out.versions + ).match() + } + ) + } + } + + test("test-hmmer-hmmbuild-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id: 'PF14720' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) + ] + input[1] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap new file mode 100644 index 000000000000..8cdff17c1420 --- /dev/null +++ b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap @@ -0,0 +1,55 @@ +{ + "test-hmmer-hmmbuild-stub": { + "content": [ + { + "0": [ + [ + { + "id": "PF14720" + }, + "PF14720.hmm.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "PF14720.hmmbuild.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "2": [ + "versions.yml:md5,6f4796b714cb0d5981cd12d9e89cb599" + ], + "hmm": [ + [ + { + "id": "PF14720" + }, + "PF14720.hmm.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "hmmbuildout": [ + "PF14720.hmmbuild.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,6f4796b714cb0d5981cd12d9e89cb599" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:38:44.751216" + }, + "test-hmmer-hmmbuild": { + "content": [ + "PF14720.hmm.gz", + "PF14720.hmmbuild.txt", + [ + "versions.yml:md5,6f4796b714cb0d5981cd12d9e89cb599" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:49:25.772308" + } +} \ No newline at end of file diff --git a/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test new file mode 100644 index 000000000000..46c7b58fcc21 --- /dev/null +++ b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test @@ -0,0 +1,115 @@ + +nextflow_process { + + name "Test Process HMMER_HMMFETCH" + script "../main.nf" + process "HMMER_HMMFETCH" + + tag "modules" + tag "modules_nfcore" + tag "hmmer" + tag "hmmer/hmmfetch" + + test("test-hmmer-hmmfetch-key") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') + ] + input[1] = '16S_rRNA' + input[2] = [] + input[3] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-hmmer-hmmfetch-keyfile") { + + when { + process { + """ + keyfile = Channel.of('16S_rRNA', '23S_rRNA').collectFile(name: 'keys.txt', newLine: true) + + input[0] = [ + [ id:'test', single_end:false ], + file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') + ] + input[1] = [] + input[2] = keyfile + input[3] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-hmmer-hmmfetch-index") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') + ] + input[1] = [] + input[2] = [] + input[3] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-hmmer-hmmfetch-index-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') + ] + input[1] = [] + input[2] = [] + input[3] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test.snap new file mode 100644 index 000000000000..d934b779abe6 --- /dev/null +++ b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test.snap @@ -0,0 +1,166 @@ +{ + "test-hmmer-hmmfetch-index": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "arc.hmm.ssi:md5,17a7bb35662baabb5b1474660d072fb6" + ] + ], + "2": [ + "versions.yml:md5,ca18131840322abff960ba5c09f91a5a" + ], + "hmm": [ + + ], + "index": [ + [ + { + "id": "test", + "single_end": false + }, + "arc.hmm.ssi:md5,17a7bb35662baabb5b1474660d072fb6" + ] + ], + "versions": [ + "versions.yml:md5,ca18131840322abff960ba5c09f91a5a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:24:45.824243" + }, + "test-hmmer-hmmfetch-index-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hmm:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,ca18131840322abff960ba5c09f91a5a" + ], + "hmm": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hmm:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "index": [ + + ], + "versions": [ + "versions.yml:md5,ca18131840322abff960ba5c09f91a5a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:24:50.535566" + }, + "test-hmmer-hmmfetch-keyfile": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hmm:md5,0e5c7e77342ec91bc6fac2a7a0228d08" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,ca18131840322abff960ba5c09f91a5a" + ], + "hmm": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hmm:md5,0e5c7e77342ec91bc6fac2a7a0228d08" + ] + ], + "index": [ + + ], + "versions": [ + "versions.yml:md5,ca18131840322abff960ba5c09f91a5a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:29:44.506723" + }, + "test-hmmer-hmmfetch-key": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hmm:md5,0328406a7469af6f24e2157b0367705f" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,ca18131840322abff960ba5c09f91a5a" + ], + "hmm": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hmm:md5,0328406a7469af6f24e2157b0367705f" + ] + ], + "index": [ + + ], + "versions": [ + "versions.yml:md5,ca18131840322abff960ba5c09f91a5a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:24:38.347449" + } +} \ No newline at end of file diff --git a/modules/nf-core/homer/annotatepeaks/environment.yml b/modules/nf-core/homer/annotatepeaks/environment.yml index aef00e188a90..f6522d695038 100644 --- a/modules/nf-core/homer/annotatepeaks/environment.yml +++ b/modules/nf-core/homer/annotatepeaks/environment.yml @@ -2,6 +2,5 @@ name: homer_annotatepeaks channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::homer=4.11 diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 32478df4124c..d3d752c8302e 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -39,4 +39,16 @@ process HOMER_ANNOTATEPEAKS { homer: $VERSION END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + touch ${prefix}.annotatePeaks.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + homer: $VERSION + END_VERSIONS + """ } diff --git a/modules/nf-core/homer/annotatepeaks/tests/main.nf.test b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test new file mode 100644 index 000000000000..e54c4b907681 --- /dev/null +++ b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test @@ -0,0 +1,68 @@ + +nextflow_process { + + name "Test Process HOMER_ANNOTATEPEAKS" + script "../main.nf" + process "HOMER_ANNOTATEPEAKS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "homer" + tag "homer/annotatepeaks" + + test("test-homer-annotatepeaks") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.txt[0][1]).name, // unstable + process.out.stats, + process.out.versions + ).match() + } + ) + } + } + + test("test-homer-annotatepeaks-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap new file mode 100644 index 000000000000..0d6c813b2b13 --- /dev/null +++ b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap @@ -0,0 +1,62 @@ +{ + "test-homer-annotatepeaks-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.annotatePeaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,d109521b6e43672cf246fd269b3833c8" + ], + "stats": [ + + ], + "txt": [ + [ + { + "id": "test" + }, + "test.annotatePeaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d109521b6e43672cf246fd269b3833c8" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:21:30.264399" + }, + "test-homer-annotatepeaks": { + "content": [ + "test.annotatePeaks.txt", + [ + [ + { + "id": "test" + }, + "test.annStats.txt:md5,eba336bce28fb5ec5d4ea3215b502dc5" + ] + ], + [ + "versions.yml:md5,d109521b6e43672cf246fd269b3833c8" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:28:26.487711" + } +} \ No newline at end of file diff --git a/modules/nf-core/homer/annotatepeaks/tests/nextflow.config b/modules/nf-core/homer/annotatepeaks/tests/nextflow.config new file mode 100644 index 000000000000..309aac551b00 --- /dev/null +++ b/modules/nf-core/homer/annotatepeaks/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = {"-annStats ${meta.id}.annStats.txt"} +} diff --git a/modules/nf-core/hypo/environment.yml b/modules/nf-core/hypo/environment.yml index dd2c6e25118b..70e432fada78 100644 --- a/modules/nf-core/hypo/environment.yml +++ b/modules/nf-core/hypo/environment.yml @@ -2,6 +2,5 @@ name: hypo channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hypo=1.0.3 diff --git a/modules/nf-core/hypo/meta.yml b/modules/nf-core/hypo/meta.yml index 36a7e714f752..002b418f5c8c 100644 --- a/modules/nf-core/hypo/meta.yml +++ b/modules/nf-core/hypo/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/kensung-lab/hypo/blob/master/README.md" tool_dev_url: "https://github.com/kensung-lab/hypo" doi: "10.1101/2019.12.19.882506" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/hypo/tests/main.nf.test b/modules/nf-core/hypo/tests/main.nf.test new file mode 100644 index 000000000000..06fb15906f07 --- /dev/null +++ b/modules/nf-core/hypo/tests/main.nf.test @@ -0,0 +1,76 @@ + +nextflow_process { + + name "Test Process HYPO" + script "../main.nf" + process "HYPO" + + tag "modules" + tag "modules_nfcore" + tag "hypo" + + test("test-hypo") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[3] = 29903 + input[4] = 5 + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-hypo-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[3] = 29903 + input[4] = 5 + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/hypo/tests/main.nf.test.snap b/modules/nf-core/hypo/tests/main.nf.test.snap new file mode 100644 index 000000000000..999ec08c13df --- /dev/null +++ b/modules/nf-core/hypo/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-hypo-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9" + ], + "fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:15:49.822312" + }, + "test-hypo": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,d326ff4fc91e25617c43d678f68187ad" + ] + ], + "1": [ + "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9" + ], + "fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,d326ff4fc91e25617c43d678f68187ad" + ] + ], + "versions": [ + "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:15:37.149543" + } +} \ No newline at end of file diff --git a/modules/nf-core/idr/environment.yml b/modules/nf-core/idr/environment.yml index 51378273997f..2790cc3fa4af 100644 --- a/modules/nf-core/idr/environment.yml +++ b/modules/nf-core/idr/environment.yml @@ -2,6 +2,5 @@ name: idr channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::idr=2.0.4.2 diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index f27c85917d8d..037435186465 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -46,4 +46,23 @@ process IDR { idr: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//') END_VERSIONS """ + + stub: + if (peaks.toList().size < 2) { + log.error "[ERROR] idr needs at least two replicates only one provided." + } + def peak_types = ['narrowPeak', 'broadPeak', 'bed'] + if (!peak_types.contains(peak_type)) { + log.error "[ERROR] Invalid option: '${peak_type}'. Valid options for 'peak_type': ${peak_types.join(', ')}." + } + """ + touch "${prefix}.idrValues.txt" + touch "${prefix}.log.txt" + touch "${prefix}.png" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + idr: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/idr/meta.yml b/modules/nf-core/idr/meta.yml index fb7c6944a4c5..5f2ab1109e38 100644 --- a/modules/nf-core/idr/meta.yml +++ b/modules/nf-core/idr/meta.yml @@ -17,15 +17,15 @@ tools: licence: ["GPL v2"] input: - peaks: - type: tuple of two files + type: list description: BED, narrowPeak or broadPeak files of replicates pattern: "*" - peak_type: - type: value + type: string description: Type of peak file pattern: "{narrowPeak,broadPeak,bed}" - prefix: - type: value + type: string description: Prefix for output files output: - versions: diff --git a/modules/nf-core/idr/tests/main.nf.test b/modules/nf-core/idr/tests/main.nf.test new file mode 100644 index 000000000000..7005be87dc40 --- /dev/null +++ b/modules/nf-core/idr/tests/main.nf.test @@ -0,0 +1,127 @@ + +nextflow_process { + + name "Test Process IDR" + script "../main.nf" + process "IDR" + + tag "modules" + tag "modules_nfcore" + tag "idr" + + test("test-idr-narrowpeak") { + + when { + process { + """ + input[0] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak', checkIfExists: true) + ] + input[1] = 'narrowPeak' + input[2] = 'test' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.idr, + file(process.out.log[0]).name, + file(process.out.png[0]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-idr-broadpeak") { + + when { + process { + """ + input[0] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/broadpeak/test.broadPeak', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak', checkIfExists: true) + ] + input[1] = 'broadPeak' + input[2] = 'test' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.idr, + file(process.out.log[0]).name, + file(process.out.png[0]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-idr-noprefix") { + + when { + process { + """ + input[0] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak', checkIfExists: true) + ] + input[1] = 'narrowPeak' + input[2] = 'test' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.idr, + file(process.out.log[0]).name, + file(process.out.png[0]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-idr-noprefix-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak', checkIfExists: true) + ] + input[1] = 'narrowPeak' + input[2] = 'test' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/idr/tests/main.nf.test.snap b/modules/nf-core/idr/tests/main.nf.test.snap new file mode 100644 index 000000000000..26b208ee17ef --- /dev/null +++ b/modules/nf-core/idr/tests/main.nf.test.snap @@ -0,0 +1,88 @@ +{ + "test-idr-noprefix": { + "content": [ + [ + "test.idrValues.txt:md5,09be837cc6abbc3eb5958b74802eea55" + ], + "test.log.txt", + "test.idrValues.txt.png", + [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:09:49.519754" + }, + "test-idr-broadpeak": { + "content": [ + [ + "test.idrValues.txt:md5,387441c716815e4caec3e70a2cc11a4a" + ], + "test.log.txt", + "test.idrValues.txt.png", + [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:09:30.946638" + }, + "test-idr-narrowpeak": { + "content": [ + [ + "test.idrValues.txt:md5,09be837cc6abbc3eb5958b74802eea55" + ], + "test.log.txt", + "test.idrValues.txt.png", + [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:09:14.769217" + }, + "test-idr-noprefix-stub": { + "content": [ + { + "0": [ + "test.idrValues.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + "test.log.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "2": [ + "test.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "3": [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ], + "idr": [ + "test.idrValues.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "log": [ + "test.log.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "png": [ + "test.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:55:35.671555" + } +} \ No newline at end of file diff --git a/modules/nf-core/ivar/consensus/environment.yml b/modules/nf-core/ivar/consensus/environment.yml index c7b87d024807..75e6ef41745f 100644 --- a/modules/nf-core/ivar/consensus/environment.yml +++ b/modules/nf-core/ivar/consensus/environment.yml @@ -2,6 +2,5 @@ name: ivar_consensus channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::ivar=1.4 + - bioconda::ivar=1.4.3 diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index 9786200e94c9..d57d17642a9b 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -4,8 +4,8 @@ process IVAR_CONSENSUS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ivar:1.4--h6b7c446_1' : - 'biocontainers/ivar:1.4--h6b7c446_1' }" + 'https://depot.galaxyproject.org/singularity/ivar:1.4.3--h43eeafb_0' : + 'biocontainers/ivar:1.4.3--h43eeafb_0' }" input: tuple val(meta), path(bam) @@ -43,4 +43,18 @@ process IVAR_CONSENSUS { ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def touch_mpileup = save_mpileup ? "touch ${prefix}.mpileup" : '' + """ + touch ${prefix}.fa + touch ${prefix}.qual.txt + $touch_mpileup + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/ivar/consensus/tests/main.nf.test b/modules/nf-core/ivar/consensus/tests/main.nf.test new file mode 100644 index 000000000000..9255bed082e6 --- /dev/null +++ b/modules/nf-core/ivar/consensus/tests/main.nf.test @@ -0,0 +1,100 @@ + +nextflow_process { + + name "Test Process IVAR_CONSENSUS" + script "../main.nf" + process "IVAR_CONSENSUS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ivar" + tag "ivar/consensus" + + test("test-ivar-consensus") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = false + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fasta, + file(process.out.qual[0][1]).name, // empty + process.out.mpileup, + process.out.versions, + file(process.out.versions[0]).readLines().collect { it.trim() } // Trap to catch conda version mismatches + ).match() + } + ) + } + } + + test("test-ivar-consensus-mpileup") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fasta, + file(process.out.qual[0][1]).name, // empty + file(process.out.mpileup[0][1]).name, // empty + process.out.versions + ).match() + } + ) + } + } + + test("test-ivar-consensus-mpileup-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/ivar/consensus/tests/main.nf.test.snap b/modules/nf-core/ivar/consensus/tests/main.nf.test.snap new file mode 100644 index 000000000000..e220ecabb5e6 --- /dev/null +++ b/modules/nf-core/ivar/consensus/tests/main.nf.test.snap @@ -0,0 +1,117 @@ +{ + "test-ivar-consensus-mpileup-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.qual.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3" + ], + "fasta": [ + [ + { + "id": "test" + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mpileup": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "qual": [ + [ + { + "id": "test" + }, + "test.qual.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:58:57.447441" + }, + "test-ivar-consensus-mpileup": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fa:md5,9e21a64818f4302b4dece5480fa5e8b8" + ] + ], + "test.qual.txt", + "test.mpileup", + [ + "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:58:52.938906" + }, + "test-ivar-consensus": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fa:md5,9e21a64818f4302b4dece5480fa5e8b8" + ] + ], + "test.qual.txt", + [ + + ], + [ + "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3" + ], + [ + "\"IVAR_CONSENSUS\":", + "ivar: 1.4.3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:58:48.289344" + } +} \ No newline at end of file diff --git a/modules/nf-core/ivar/consensus/tests/nextflow.config b/modules/nf-core/ivar/consensus/tests/nextflow.config new file mode 100644 index 000000000000..e34c650406f9 --- /dev/null +++ b/modules/nf-core/ivar/consensus/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: IVAR_CONSENSUS { + ext.args2 = '-aa -A -d 0 -Q 0' + } +} diff --git a/modules/nf-core/ivar/variants/environment.yml b/modules/nf-core/ivar/variants/environment.yml index 7431cac4ff1a..6b1443eb15ff 100644 --- a/modules/nf-core/ivar/variants/environment.yml +++ b/modules/nf-core/ivar/variants/environment.yml @@ -2,6 +2,5 @@ name: ivar_variants channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::ivar=1.4 + - bioconda::ivar=1.4.3 diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index 189696aaf6a5..e8831ba937f7 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -4,8 +4,8 @@ process IVAR_VARIANTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ivar:1.4--h6b7c446_1' : - 'biocontainers/ivar:1.4--h6b7c446_1' }" + 'https://depot.galaxyproject.org/singularity/ivar:1.4.3--h43eeafb_0' : + 'biocontainers/ivar:1.4.3--h43eeafb_0' }" input: tuple val(meta), path(bam) @@ -44,7 +44,20 @@ process IVAR_VARIANTS { cat <<-END_VERSIONS > versions.yml "${task.process}": - ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//') + ivar: \$(ivar version | sed 's/^.*iVar version //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def touch_mpileup = save_mpileup ? "touch ${prefix}.mpileup" : '' + """ + touch ${prefix}.tsv + $touch_mpileup + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ivar: \$(ivar version | sed 's/^.*iVar version //; s/ .*\$//') END_VERSIONS """ } diff --git a/modules/nf-core/ivar/variants/tests/main.nf.test b/modules/nf-core/ivar/variants/tests/main.nf.test new file mode 100644 index 000000000000..35a440bf5a0e --- /dev/null +++ b/modules/nf-core/ivar/variants/tests/main.nf.test @@ -0,0 +1,118 @@ + +nextflow_process { + + name "Test Process IVAR_VARIANTS" + script "../main.nf" + process "IVAR_VARIANTS" + + tag "modules" + tag "modules_nfcore" + tag "ivar" + tag "ivar/variants" + + test("test-ivar-variants-no-gff-no-mpileup") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = [] + input[4] = false + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-ivar-variants-no-gff-with-mpileup") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = [] + input[4] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-ivar-variants-with-gff-with-mpileup") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) + input[4] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-ivar-variants-with-gff-with-mpileup-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) + input[4] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/ivar/variants/tests/main.nf.test.snap b/modules/nf-core/ivar/variants/tests/main.nf.test.snap new file mode 100644 index 000000000000..75ab31634cb7 --- /dev/null +++ b/modules/nf-core/ivar/variants/tests/main.nf.test.snap @@ -0,0 +1,188 @@ +{ + "test-ivar-variants-no-gff-no-mpileup": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,76c93420121bb891fa275f716142a157" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ], + "mpileup": [ + + ], + "tsv": [ + [ + { + "id": "test" + }, + "test.tsv:md5,76c93420121bb891fa275f716142a157" + ] + ], + "versions": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:00:35.649607" + }, + "test-ivar-variants-with-gff-with-mpileup": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,2cf6c48b55e0e81155ff310d48de94df" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,958e6bead4103d72026f80153b6b5150" + ] + ], + "2": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ], + "mpileup": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,958e6bead4103d72026f80153b6b5150" + ] + ], + "tsv": [ + [ + { + "id": "test" + }, + "test.tsv:md5,2cf6c48b55e0e81155ff310d48de94df" + ] + ], + "versions": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:00:48.194076" + }, + "test-ivar-variants-with-gff-with-mpileup-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ], + "mpileup": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tsv": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:00:52.839222" + }, + "test-ivar-variants-no-gff-with-mpileup": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,76c93420121bb891fa275f716142a157" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,958e6bead4103d72026f80153b6b5150" + ] + ], + "2": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ], + "mpileup": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,958e6bead4103d72026f80153b6b5150" + ] + ], + "tsv": [ + [ + { + "id": "test" + }, + "test.tsv:md5,76c93420121bb891fa275f716142a157" + ] + ], + "versions": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:00:41.680848" + } +} \ No newline at end of file diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml new file mode 100644 index 000000000000..cf7e84012ee9 --- /dev/null +++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "jvarkit_vcfpolyx" +channels: + - bioconda + - conda-forge +dependencies: + - "bioconda::jvarkit=2024.08.25" diff --git a/modules/nf-core/jvarkit/vcfpolyx/main.nf b/modules/nf-core/jvarkit/vcfpolyx/main.nf new file mode 100644 index 000000000000..77005f6fc469 --- /dev/null +++ b/modules/nf-core/jvarkit/vcfpolyx/main.nf @@ -0,0 +1,65 @@ +process JVARKIT_VCFPOLYX { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_1': + 'biocontainers/jvarkit:2024.08.25--hdfd78af_1' }" + + input: + tuple val(meta), path(vcf) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + + output: + tuple val(meta), path("*.${extension}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args1 = task.ext.args1 ?: '' + def args2 = meta.vcfpolyx_args ?: (task.ext.args2 ?: ' --tag POLYX --max-repeats 10 ') + def args3 = task.ext.args3 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + extension = args3.contains("--output-type b") || args3.contains("-Ob") ? "bcf.gz" : + args3.contains("--output-type u") || args3.contains("-Ou") ? "bcf" : + args3.contains("--output-type z") || args3.contains("-Oz") ? "vcf.gz" : + args3.contains("--output-type v") || args3.contains("-Ov") ? "vcf" : + "vcf" + + if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + """ + mkdir -p TMP + + bcftools view -O v ${args1} "${vcf}" |\\ + jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx --reference "${fasta}" ${args2} |\\ + bcftools view --output "${prefix}.${extension}" ${args3} + + rm -rf TMP + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch "${prefix}.${extension}" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ +} diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml new file mode 100644 index 000000000000..221f7e9ca516 --- /dev/null +++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml @@ -0,0 +1,94 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "jvarkit_vcfpolyx" +description: annotate VCF files for poly repeats +keywords: + - vcf + - bcf + - annotation + - repeats +tools: + - "jvarkit": + description: "Java utilities for Bioinformatics." + homepage: "https://github.com/lindenb/jvarkit" + documentation: "https://jvarkit.readthedocs.io/" + tool_dev_url: "https://github.com/lindenb/jvarkit" + doi: "10.6084/m9.figshare.1425030" + licence: ["MIT License"] + + - "bcftools": + description: | + View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF + homepage: "http://samtools.github.io/bcftools/bcftools.html" + documentation: "http://www.htslib.org/doc/bcftools.html" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing VCF information + + - meta2: + type: map + description: | + Groovy Map containing fasta information + + - meta3: + type: map + description: | + Groovy Map containing fasta.fai information + + - meta4: + type: map + description: | + Groovy Map containing fasta.dict information + + - vcf: + type: file + description: Groovy Map containing reference genome information for vcf + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + + - fasta: + type: file + description: Groovy Map containing reference genome information for fai reference fasta file + pattern: "*.fasta" + + - fai: + type: file + description: Groovy Map containing reference genome information for fai + pattern: "*.fasta.fai" + + - dict: + type: file + description: Groovy Map containing reference genome information for GATK sequence dictionary + pattern: "*.dict" + +output: + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF filtered output file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@lindenb" +maintainers: + - "@lindenb" diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test new file mode 100644 index 000000000000..72ec3a71473d --- /dev/null +++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test @@ -0,0 +1,43 @@ +// nf-core modules test jvarkit/vcfpolyx +nextflow_process { + + name "Test Process JVARKIT_VCFPOLYX" + script "../main.nf" + process "JVARKIT_VCFPOLYX" + + tag "modules" + tag "modules_nfcore" + tag "jvarkit" + tag "jvarkit/vcfpolyx" + + test("sarscov2 - vcf") { + + when { + process { + """ + input[0] =[ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + process.out.versions + ).match() + } + ) + } + + } + + +} diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap new file mode 100644 index 000000000000..e5ccf1914720 --- /dev/null +++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "sarscov2 - vcf": { + "content": [ + "65a03a6057dc74467c2b7b17230e7f14", + [ + "versions.yml:md5,b3c351a56da9062295ef90011a9cd48c" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + } +} diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/tags.yml b/modules/nf-core/jvarkit/vcfpolyx/tests/tags.yml new file mode 100644 index 000000000000..475476a589b1 --- /dev/null +++ b/modules/nf-core/jvarkit/vcfpolyx/tests/tags.yml @@ -0,0 +1,2 @@ +jvarkit/vcfpolyx: + - "modules/nf-core/jvarkit/vcfpolyx/**" diff --git a/modules/nf-core/legsta/environment.yml b/modules/nf-core/legsta/environment.yml index 34d11fcfbe37..ae157ec4a905 100644 --- a/modules/nf-core/legsta/environment.yml +++ b/modules/nf-core/legsta/environment.yml @@ -2,6 +2,5 @@ name: legsta channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::legsta=0.5.1 diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index d28d01bbb3e2..d776d64153f1 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -30,4 +30,15 @@ process LEGSTA { legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;') + END_VERSIONS + """ } diff --git a/modules/nf-core/legsta/meta.yml b/modules/nf-core/legsta/meta.yml index 399438332392..734498e06126 100644 --- a/modules/nf-core/legsta/meta.yml +++ b/modules/nf-core/legsta/meta.yml @@ -3,6 +3,8 @@ description: Typing of clinical and environmental isolates of Legionella pneumop keywords: - bacteria - legionella + - clinical + - pneumophila tools: - legsta: description: In silico Legionella pneumophila Sequence Based Typing diff --git a/modules/nf-core/legsta/tests/main.nf.test b/modules/nf-core/legsta/tests/main.nf.test new file mode 100644 index 000000000000..bed639db0a6b --- /dev/null +++ b/modules/nf-core/legsta/tests/main.nf.test @@ -0,0 +1,57 @@ + +nextflow_process { + + name "Test Process LEGSTA" + script "../main.nf" + process "LEGSTA" + + tag "modules" + tag "modules_nfcore" + tag "legsta" + + test("test-legsta") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-legsta-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/legsta/tests/main.nf.test.snap b/modules/nf-core/legsta/tests/main.nf.test.snap new file mode 100644 index 000000000000..54adc1906f77 --- /dev/null +++ b/modules/nf-core/legsta/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-legsta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,c493bdd19335de4828aa8b4e3ce7e1f8" + ] + ], + "1": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,c493bdd19335de4828aa8b4e3ce7e1f8" + ] + ], + "versions": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:09:21.017956" + }, + "test-legsta-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:09:26.594828" + } +} \ No newline at end of file diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index ef472f4a737e..7389e7b597b1 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -49,4 +49,17 @@ process MAPDAMAGE2 { mapdamage2: \$(echo \$(mapDamage --version)) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir results_${bam.baseName} + + touch results_${bam.baseName}/Runtime_log.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mapdamage2: \$(echo \$(mapDamage --version)) + END_VERSIONS + """ } diff --git a/modules/nf-core/mapdamage2/tests/main.nf.test b/modules/nf-core/mapdamage2/tests/main.nf.test new file mode 100644 index 000000000000..5c3e1a42bc4f --- /dev/null +++ b/modules/nf-core/mapdamage2/tests/main.nf.test @@ -0,0 +1,80 @@ + +nextflow_process { + + name "Test Process MAPDAMAGE2" + script "../main.nf" + process "MAPDAMAGE2" + + tag "modules" + tag "modules_nfcore" + tag "mapdamage2" + + test("test-mapdamage2") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.runtime_log[0][1]).name, + file(process.out.fragmisincorporation_plot[0][1]).name, + process.out.length_plot, + file(process.out.misincorporation[0][1]).readLines()[3..7], + file(process.out.lgdistribution[0][1]).readLines()[0], + file(process.out.dnacomp[0][1]).readLines()[3..7], + file(process.out.stats_out_mcmc_hist[0][1]).name, + file(process.out.stats_out_mcmc_iter[0][1]).name, + file(process.out.stats_out_mcmc_trace[0][1]).name, + file(process.out.stats_out_mcmc_iter_summ_stat[0][1]).name, + file(process.out.stats_out_mcmc_post_pred[0][1]).name, + file(process.out.stats_out_mcmc_correct_prob[0][1]).name, + process.out.dnacomp_genome, + process.out.rescaled, + file(process.out.pctot_freq[0][1]).readLines()[3..7], + file(process.out.pgtoa_freq[0][1]).readLines()[3..7], + process.out.fasta, + process.out.folder, + process.out.versions + ).match() + } + ) + } + } + + test("test-mapdamage2-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/mapdamage2/tests/main.nf.test.snap b/modules/nf-core/mapdamage2/tests/main.nf.test.snap new file mode 100644 index 000000000000..b80a180dd792 --- /dev/null +++ b/modules/nf-core/mapdamage2/tests/main.nf.test.snap @@ -0,0 +1,209 @@ +{ + "test-mapdamage2-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "Runtime_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + + ], + "13": [ + + ], + "14": [ + + ], + "15": [ + + ], + "16": [ + + ], + "17": [ + + ], + "18": [ + "versions.yml:md5,0b723ea4deee4a620ca29347bc3bbb05" + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "dnacomp": [ + + ], + "dnacomp_genome": [ + + ], + "fasta": [ + + ], + "folder": [ + + ], + "fragmisincorporation_plot": [ + + ], + "length_plot": [ + + ], + "lgdistribution": [ + + ], + "misincorporation": [ + + ], + "pctot_freq": [ + + ], + "pgtoa_freq": [ + + ], + "rescaled": [ + + ], + "runtime_log": [ + [ + { + "id": "test", + "single_end": false + }, + "Runtime_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats_out_mcmc_correct_prob": [ + + ], + "stats_out_mcmc_hist": [ + + ], + "stats_out_mcmc_iter": [ + + ], + "stats_out_mcmc_iter_summ_stat": [ + + ], + "stats_out_mcmc_post_pred": [ + + ], + "stats_out_mcmc_trace": [ + + ], + "versions": [ + "versions.yml:md5,0b723ea4deee4a620ca29347bc3bbb05" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:05:58.359113" + }, + "test-mapdamage2": { + "content": [ + "Runtime_log.txt", + "Fragmisincorporation_plot.pdf", + [ + + ], + [ + "Chr\tEnd\tStd\tPos\tA\tC\tG\tT\tTotal\tG>A\tC>T\tA>G\tT>C\tA>C\tA>T\tC>G\tC>A\tT>G\tT>A\tG>C\tG>T\tA>-\tT>-\tC>-\tG>-\t->A\t->T\t->C\t->G\tS", + "chr22\t3p\t+\t1\t880\t514\t382\t1043\t2819\t0\t0\t0\t0\t0\t1\t1\t2\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t11", + "chr22\t3p\t+\t2\t879\t509\t409\t1023\t2820\t0\t0\t0\t1\t0\t0\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11", + "chr22\t3p\t+\t3\t874\t507\t404\t1035\t2820\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t10", + "chr22\t3p\t+\t4\t903\t538\t377\t1002\t2820\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8" + ], + "# table produced by mapDamage version 2.2.1", + [ + "Chr\tEnd\tStd\tPos\tA\tC\tG\tT\tTotal", + "chr22\t3p\t+\t-70\t790\t444\t460\t1077\t2771", + "chr22\t3p\t+\t-69\t817\t404\t481\t1074\t2776", + "chr22\t3p\t+\t-68\t772\t379\t487\t1142\t2780", + "chr22\t3p\t+\t-67\t776\t398\t487\t1123\t2784" + ], + "Stats_out_MCMC_hist.pdf", + "Stats_out_MCMC_iter.csv", + "Stats_out_MCMC_trace.pdf", + "Stats_out_MCMC_iter_summ_stat.csv", + "Stats_out_MCMC_post_pred.pdf", + "Stats_out_MCMC_correct_prob.csv", + [ + [ + { + "id": "test", + "single_end": false + }, + "dnacomp_genome.csv:md5,ea91a3d205717d3c6b3e0b77bb840945" + ] + ], + [ + + ], + [ + "3\t0.00133511348464619", + "4\t0.00134770889487871", + "5\t0.0014367816091954", + "6\t0", + "7\t0" + ], + [ + "3\t0", + "4\t0", + "5\t0.00145348837209302", + "6\t0", + "7\t0" + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,0b723ea4deee4a620ca29347bc3bbb05" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:43:22.92724" + } +} \ No newline at end of file diff --git a/modules/nf-core/mirtrace/qc/main.nf b/modules/nf-core/mirtrace/qc/main.nf index ac9575bb35c2..9d047a7a1e36 100644 --- a/modules/nf-core/mirtrace/qc/main.nf +++ b/modules/nf-core/mirtrace/qc/main.nf @@ -25,7 +25,6 @@ process MIRTRACE_QC { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def file_list = reads.collect { it.toString() } """ mirtrace qc \\ @@ -33,7 +32,7 @@ process MIRTRACE_QC { --write-fasta \\ --output-dir . \\ --force \\ - ${file_list.join(' ')} + ${reads} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/mirtrace/qc/tests/main.nf.test b/modules/nf-core/mirtrace/qc/tests/main.nf.test index ea2f99fbf2f4..9ce14fd468c3 100644 --- a/modules/nf-core/mirtrace/qc/tests/main.nf.test +++ b/modules/nf-core/mirtrace/qc/tests/main.nf.test @@ -17,8 +17,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] ] input[1] = "hsa" diff --git a/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap b/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap index 7f7f3742e298..22efdd9e9b9b 100644 --- a/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap +++ b/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap @@ -7,10 +7,7 @@ "id": "test", "single_end": false }, - [ - "test_rnaseq_1.fasta:md5,0181296141177654088bbc2a96b29560", - "test_rnaseq_2.fasta:md5,302d432f8b5cbf6556e1143679c42847" - ] + "test_rnaseq_1.fasta:md5,0181296141177654088bbc2a96b29560" ] ] ], @@ -18,7 +15,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T13:42:28.226466479" + "timestamp": "2024-09-05T18:05:42.043272808" }, "versions": { "content": [ @@ -41,13 +38,13 @@ "single_end": false }, [ - "mirtrace-stats-contamination_basic.tsv:md5,b668899b3ad2f006e073474122103b7a", - "mirtrace-stats-contamination_detailed.tsv:md5,84437ccb74715e956fab549f0567c5c9", - "mirtrace-stats-length.tsv:md5,37a0d254fdb800a0467c8fba7215d724", - "mirtrace-stats-mirna-complexity.tsv:md5,12cebc277d1d7873e4cb707291a82dd2", - "mirtrace-stats-phred.tsv:md5,118bbdc67433ce6fd38c74c37b0fcd3b", - "mirtrace-stats-qcstatus.tsv:md5,6bf4bf54faca386a74bb92592ae4f8ba", - "mirtrace-stats-rnatype.tsv:md5,10ec4e1ad0837efeecc97913cbab5d0f" + "mirtrace-stats-contamination_basic.tsv:md5,ac69ca6d2a709854f1048b635d06e927", + "mirtrace-stats-contamination_detailed.tsv:md5,ef80997ac12662c64cbcf5fe9851e786", + "mirtrace-stats-length.tsv:md5,54ecc0698e8e83d5b1c979b2ee3b1512", + "mirtrace-stats-mirna-complexity.tsv:md5,ab2a7600a2daa5c1797eea13d0abc2f0", + "mirtrace-stats-phred.tsv:md5,44eaeae26ec629e71fb31e56bfb5a548", + "mirtrace-stats-qcstatus.tsv:md5,623cf3a0c5e363488966844feb0dd978", + "mirtrace-stats-rnatype.tsv:md5,ed8d3a76247a1432a365def87c3f4c67" ] ] ] @@ -56,7 +53,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T13:42:28.194166262" + "timestamp": "2024-09-05T18:05:41.888457948" }, "human - fastq - stub": { "content": [ @@ -173,10 +170,7 @@ "id": "test", "single_end": false }, - [ - "test_rnaseq_1.fasta:md5,0181296141177654088bbc2a96b29560", - "test_rnaseq_2.fasta:md5,302d432f8b5cbf6556e1143679c42847" - ] + "test_rnaseq_1.fasta:md5,0181296141177654088bbc2a96b29560" ] ] ], @@ -184,6 +178,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T13:42:28.208336131" + "timestamp": "2024-09-05T18:05:41.978281344" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/createtsv/environment.yml b/modules/nf-core/mmseqs/createtsv/environment.yml index 4840fc02945a..6f1bd86b3120 100644 --- a/modules/nf-core/mmseqs/createtsv/environment.yml +++ b/modules/nf-core/mmseqs/createtsv/environment.yml @@ -2,6 +2,5 @@ name: mmseqs_createtsv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/databases/environment.yml b/modules/nf-core/mmseqs/databases/environment.yml index 3bf8437d228f..cad92fadd85f 100644 --- a/modules/nf-core/mmseqs/databases/environment.yml +++ b/modules/nf-core/mmseqs/databases/environment.yml @@ -2,6 +2,5 @@ name: mmseqs_databases channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/databases/main.nf b/modules/nf-core/mmseqs/databases/main.nf index 3e228b29d511..d43681cea94d 100644 --- a/modules/nf-core/mmseqs/databases/main.nf +++ b/modules/nf-core/mmseqs/databases/main.nf @@ -11,8 +11,8 @@ process MMSEQS_DATABASES { val database output: - path "${prefix}/" , emit: database - path "versions.yml" , emit: versions + path "${prefix}/" , emit: database + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test b/modules/nf-core/mmseqs/databases/tests/main.nf.test new file mode 100644 index 000000000000..3fe5d20069de --- /dev/null +++ b/modules/nf-core/mmseqs/databases/tests/main.nf.test @@ -0,0 +1,55 @@ + +nextflow_process { + + name "Test Process MMSEQS_DATABASES" + script "../main.nf" + process "MMSEQS_DATABASES" + + tag "modules" + tag "modules_nfcore" + tag "mmseqs" + tag "mmseqs/databases" + + test("test-mmseqs-databases") { + + when { + process { + """ + input[0] = "SILVA" + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.database[0]).listFiles().collect { it.name }.toSorted(), // unstable + process.out.versions + ).match() + } + ) + } + } + + test("test-mmseqs-databases-stub") { + options '-stub' + when { + process { + """ + input[0] = "SILVA" + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap new file mode 100644 index 000000000000..00d3003ebbcb --- /dev/null +++ b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap @@ -0,0 +1,74 @@ +{ + "test-mmseqs-databases": { + "content": [ + [ + "database", + "database.dbtype", + "database.index", + "database.lookup", + "database.source", + "database.version", + "database_h", + "database_h.dbtype", + "database_h.index", + "database_mapping", + "database_taxonomy" + ], + [ + "versions.yml:md5,b038db45e5934b8f0f743449bbac01b4" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:43:58.454012" + }, + "test-mmseqs-databases-stub": { + "content": [ + { + "0": [ + [ + "database:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.index:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.lookup:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.source:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.version:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h.index:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_mapping:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,49082428ec974e4ddb09a6ca2e9f21b3" + ], + "database": [ + [ + "database:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.index:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.lookup:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.source:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.version:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h.index:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_mapping:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,49082428ec974e4ddb09a6ca2e9f21b3" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T17:00:20.527628" + } +} \ No newline at end of file diff --git a/modules/nf-core/mmseqs/taxonomy/environment.yml b/modules/nf-core/mmseqs/taxonomy/environment.yml index fa40c2770e1f..89bc7c503d60 100644 --- a/modules/nf-core/mmseqs/taxonomy/environment.yml +++ b/modules/nf-core/mmseqs/taxonomy/environment.yml @@ -4,6 +4,5 @@ name: "mmseqs_taxonomy" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::mmseqs2=15.6f452" diff --git a/modules/nf-core/orthofinder/environment.yml b/modules/nf-core/orthofinder/environment.yml index f93b9bb0e885..4239c4c18154 100644 --- a/modules/nf-core/orthofinder/environment.yml +++ b/modules/nf-core/orthofinder/environment.yml @@ -1,9 +1,7 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "orthofinder" +name: orthofinder channels: - conda-forge - bioconda - - defaults dependencies: - - "bioconda::orthofinder=2.5.5" + - bioconda::diamond=2.1.9 + - bioconda::orthofinder=2.5.5 diff --git a/modules/nf-core/orthofinder/main.nf b/modules/nf-core/orthofinder/main.nf index 2971fc0acf8b..a47c4dea36c2 100644 --- a/modules/nf-core/orthofinder/main.nf +++ b/modules/nf-core/orthofinder/main.nf @@ -9,31 +9,40 @@ process ORTHOFINDER { input: tuple val(meta), path(fastas, stageAs: 'input/') + tuple val(meta2), path(prior_run) output: - tuple val(meta), path("$prefix") , emit: orthofinder - path "versions.yml" , emit: versions + tuple val(meta), path("$prefix") , emit: orthofinder + tuple val(meta), path("$prefix/WorkingDirectory") , emit: working + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def include_command = prior_run ? "-b $prior_run" : '' + """ mkdir temp_pickle orthofinder \\ - $args \\ -t $task.cpus \\ -a $task.cpus \\ -p temp_pickle \\ -f input \\ - -n $prefix + -n $prefix \\ + $include_command \\ + $args + + if [ -e input/OrthoFinder/Results_$prefix ]; then + mv input/OrthoFinder/Results_$prefix $prefix + fi - mv \\ - input/OrthoFinder/Results_$prefix \\ - $prefix + if [ -e ${prior_run}/OrthoFinder/Results_$prefix ]; then + mv ${prior_run}/OrthoFinder/Results_$prefix $prefix + fi cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -42,8 +51,10 @@ process ORTHOFINDER { """ stub: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def include_command = prior_run ? "-b $prior_run" : '' + """ mkdir -p $prefix/Comparative_Genomics_Statistics mkdir $prefix/Gene_Duplication_Events diff --git a/modules/nf-core/orthofinder/meta.yml b/modules/nf-core/orthofinder/meta.yml index 23cc5320bcb3..8c7689b3e86d 100644 --- a/modules/nf-core/orthofinder/meta.yml +++ b/modules/nf-core/orthofinder/meta.yml @@ -29,6 +29,15 @@ input: type: list description: Input fasta files pattern: "*.{fa,faa,fasta,fas,pep}" + - meta2: + type: map + description: | + Groovy Map containing a name + e.g. `[ id:'folder1' ]` + - prior_run: + type: directory + description: | + A folder container containing a previous WorkingDirectory from Orthofinder. output: - meta: @@ -43,6 +52,9 @@ output: - orthofinder: type: directory description: Orthofinder output directory + - working: + type: directory + description: Orthofinder output WorkingDirectory (used for the orthofinder resume function) authors: - "@GallVp" diff --git a/modules/nf-core/orthofinder/tests/main.nf.test b/modules/nf-core/orthofinder/tests/main.nf.test index 2d648004b063..aa68d1d21abb 100644 --- a/modules/nf-core/orthofinder/tests/main.nf.test +++ b/modules/nf-core/orthofinder/tests/main.nf.test @@ -9,6 +9,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "orthofinder" + tag "untar" test("sarscov2 - candidatus_portiera_aleyrodidarum - proteome") { @@ -28,6 +29,10 @@ nextflow_process { [ id:'test', single_end:false ], [ file_a, file_b ] ] + input[1] = [ + [], + [] + ] """ } } @@ -41,8 +46,6 @@ nextflow_process { all_files << file } - def all_file_names = all_files.collect { it.name }.sort(false) - def stable_file_names = [ 'Statistics_PerSpecies.tsv', 'SpeciesTree_Gene_Duplications_0.5_Support.txt', @@ -52,8 +55,66 @@ nextflow_process { def stable_files = all_files.findAll { it.name in stable_file_names } assert snapshot( - all_file_names, - stable_files, + stable_files.toSorted(), + process.out.versions[0] + ).match() + } + + } + + + test("sarscov2 - candidatus_portiera_aleyrodidarum - proteome - resume") { + + + setup { + run("UNTAR") { + script "../../untar/main.nf" + process { + """ + input[0] = [ [ id:'test1' ], // meta map + file(params.modules_testdata_base_path + 'delete_me/orthofinder/WorkingDirectory.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) + .copyTo("${workDir}/sarscov2.fasta") + + def file_a = file("https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/sequences/H1065.fasta") + def file_c = UNTAR.out.untar + input[0] = [ + [ id:'test_2', single_end:false ], + [ file_a ] + ] + input[1] = UNTAR.out.untar + """ + } + } + + then { + assert process.success + + def all_files = [] + + file(process.out.orthofinder[0][1]).eachFileRecurse (FileType.FILES) { file -> + all_files << file + } + + def stable_file_names = [ + 'Statistics_PerSpecies.tsv', + 'OrthologuesStats_Totals.tsv', + 'Duplications_per_Species_Tree_Node.tsv' + ] + + def stable_files = all_files.findAll { it.name in stable_file_names } + + assert snapshot( + stable_files.toSorted(), process.out.versions[0] ).match() } @@ -80,6 +141,10 @@ nextflow_process { [ id:'test', single_end:false ], [ file_a, file_b ] ] + input[1] = [ + [], + [] + ] """ } } diff --git a/modules/nf-core/orthofinder/tests/main.nf.test.snap b/modules/nf-core/orthofinder/tests/main.nf.test.snap index 8b621c052b57..f2c7b9168146 100644 --- a/modules/nf-core/orthofinder/tests/main.nf.test.snap +++ b/modules/nf-core/orthofinder/tests/main.nf.test.snap @@ -1,310 +1,6 @@ { "sarscov2 - candidatus_portiera_aleyrodidarum - proteome": { "content": [ - [ - "Blast0_0.txt.gz", - "Blast0_1.txt.gz", - "Blast1_0.txt.gz", - "Blast1_1.txt.gz", - "Citation.txt", - "Duplications.tsv", - "Duplications_per_Orthogroup.tsv", - "Duplications_per_Species_Tree_Node.tsv", - "Log.txt", - "N0.tsv", - "OG0000000.fa", - "OG0000000_tree.txt", - "OG0000000_tree.txt", - "OG0000000_tree_id.txt", - "OG0000001.fa", - "OG0000001_tree.txt", - "OG0000001_tree.txt", - "OG0000001_tree_id.txt", - "OG0000002.fa", - "OG0000003.fa", - "OG0000004.fa", - "OG0000005.fa", - "OG0000006.fa", - "OG0000007.fa", - "OG0000008.fa", - "OG0000009.fa", - "OG0000010.fa", - "OG0000011.fa", - "OG0000012.fa", - "OG0000013.fa", - "OG0000014.fa", - "OG0000015.fa", - "OG0000016.fa", - "OG0000017.fa", - "OG0000018.fa", - "OG0000019.fa", - "OG0000020.fa", - "OG0000021.fa", - "OG0000022.fa", - "OG0000023.fa", - "OG0000024.fa", - "OG0000025.fa", - "OG0000026.fa", - "OG0000027.fa", - "OG0000028.fa", - "OG0000029.fa", - "OG0000030.fa", - 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"OG0000199.fa", - "OG0000200.fa", - "OG0000201.fa", - "OG0000202.fa", - "OG0000203.fa", - "OG0000204.fa", - "OG0000205.fa", - "OG0000206.fa", - "OG0000207.fa", - "OG0000208.fa", - "OG0000209.fa", - "OG0000210.fa", - "OG0000211.fa", - "OG0000212.fa", - "OG0000213.fa", - "OG0000214.fa", - "OG0000215.fa", - "OG0000216.fa", - "OG0000217.fa", - "OG0000218.fa", - "OG0000219.fa", - "OG0000220.fa", - "OG0000221.fa", - "OG0000222.fa", - "OG0000223.fa", - "OG0000224.fa", - "OG0000225.fa", - "OG0000226.fa", - "OG0000227.fa", - "OG0000228.fa", - "OG0000229.fa", - "OG0000230.fa", - "OG0000231.fa", - "OG0000232.fa", - "OG0000233.fa", - "OG0000234.fa", - "OG0000235.fa", - "OG0000236.fa", - "OG0000237.fa", - "OG0000238.fa", - "OG0000239.fa", - "OG0000240.fa", - "OG0000241.fa", - "OG0000242.fa", - "OG0000243.fa", - "OG0000244.fa", - "OG0000245.fa", - "OrthoFinder_graph.txt", - "Orthogroups.GeneCount.tsv", - "Orthogroups.tsv", - "Orthogroups.txt", - "Orthogroups_SingleCopyOrthologues.txt", - "Orthogroups_SpeciesOverlaps.tsv", - "Orthogroups_UnassignedGenes.tsv", - "OrthologuesStats_Totals.tsv", - "OrthologuesStats_many-to-many.tsv", - "OrthologuesStats_many-to-one.tsv", - "OrthologuesStats_one-to-many.tsv", - "OrthologuesStats_one-to-one.tsv", - "SequenceIDs.txt", - "SimpleTest.phy", - "SimpleTest.phy_fastme_stat.txt", - "SimpleTest.tre", - "Species0.fa", - "Species0.fa", - "Species1.fa", - "SpeciesIDs.txt", - "SpeciesTree_Gene_Duplications_0.5_Support.txt", - "SpeciesTree_rooted.txt", - "SpeciesTree_rooted_ids.txt", - "SpeciesTree_rooted_node_labels.txt", - "SpeciesTree_unrooted.txt", - "SpeciesTree_unrooted_ids.txt", - "Statistics_Overall.tsv", - "Statistics_PerSpecies.tsv", - "candidatus_portiera_aleyrodidarum.tsv", - "candidatus_portiera_aleyrodidarum.tsv", - "candidatus_portiera_aleyrodidarum__v__sarscov2.tsv", - "clusters_OrthoFinder_I1.5.txt", - "clusters_OrthoFinder_I1.5.txt_id_pairs.txt", - "diamondDBSpecies0.dmnd", - "diamondDBSpecies0.dmnd", - "diamondDBSpecies1.dmnd", - "sarscov2.tsv", - "sarscov2.tsv", - "sarscov2__v__candidatus_portiera_aleyrodidarum.tsv", - "test_search_results.txt.gz" - ], [ "Statistics_PerSpecies.tsv:md5,984b5011a34d54527fe17896bfa36a2d", "SpeciesTree_Gene_Duplications_0.5_Support.txt:md5,8b7a673e2e8b6d1aeb697f2bb88afa18", @@ -313,10 +9,10 @@ "versions.yml:md5,86b472c85626aac1840eec0769016f5c" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-07T21:33:50.902329" + "timestamp": "2024-09-03T10:59:02.895708598" }, "sarscov2 - candidatus_portiera_aleyrodidarum - proteome - stub": { "content": [ @@ -372,6 +68,17 @@ ] ], "1": [ + [ + { + "id": "test", + "single_end": false + }, + [ + + ] + ] + ], + "2": [ "versions.yml:md5,86b472c85626aac1840eec0769016f5c" ], "orthofinder": [ @@ -426,13 +133,39 @@ ], "versions": [ "versions.yml:md5,86b472c85626aac1840eec0769016f5c" + ], + "working": [ + [ + { + "id": "test", + "single_end": false + }, + [ + + ] + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T11:07:31.319665056" + }, + "sarscov2 - candidatus_portiera_aleyrodidarum - proteome - resume": { + "content": [ + [ + "Duplications_per_Species_Tree_Node.tsv:md5,addc6f5ceec40bd82b00038d1872a27c", + "OrthologuesStats_Totals.tsv:md5,20d243abef226051a43cb37e922fc3eb", + "Statistics_PerSpecies.tsv:md5,83174c383b6c6828d1cc9b3be1679890" + ], + "versions.yml:md5,86b472c85626aac1840eec0769016f5c" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-07T16:00:56.530716" + "timestamp": "2024-09-03T11:04:10.916947006" } } \ No newline at end of file diff --git a/modules/nf-core/paraphase/environment.yml b/modules/nf-core/paraphase/environment.yml index 3c9f5526bc48..64b4a9172dcc 100644 --- a/modules/nf-core/paraphase/environment.yml +++ b/modules/nf-core/paraphase/environment.yml @@ -3,7 +3,6 @@ name: paraphase channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::minimap2=2.28 diff --git a/modules/nf-core/paraphase/main.nf b/modules/nf-core/paraphase/main.nf index ddaa33ec04d5..8474427e66c0 100644 --- a/modules/nf-core/paraphase/main.nf +++ b/modules/nf-core/paraphase/main.nf @@ -14,17 +14,20 @@ process PARAPHASE { tuple val(meta3), path(config) output: - tuple val(meta), path("*.paraphase.json") , emit: json - tuple val(meta), path("*.paraphase.bam") , emit: bam - tuple val(meta), path("*.paraphase.bam.bai") , emit: bai - tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf"), emit: vcf, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.paraphase.json") , emit: json + tuple val(meta), path("*.paraphase.bam") , emit: bam + tuple val(meta), path("*.paraphase.bam.bai") , emit: bai + tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz") , emit: vcf , optional: true + tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}"), emit: vcf_index, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' prefix = task.ext.prefix ?: "${meta.id}" def config_file = config ? "--config $config" : "" """ @@ -37,6 +40,18 @@ process PARAPHASE { $config_file \\ --out . + for vcf in ${prefix}_paraphase_vcfs/*.vcf; + do + bgzip \\ + $args2 \\ + --threads $task.cpus \\ + \$vcf; + tabix \\ + $args3 \\ + --threads $task.cpus \\ + \$vcf.gz; + done + cat <<-END_VERSIONS > versions.yml "${task.process}": minimap2: \$(minimap2 --version 2>&1) @@ -46,15 +61,18 @@ process PARAPHASE { """ stub: - def args = task.ext.args ?: '' + def args3 = task.ext.args3 ?: '' prefix = task.ext.prefix ?: "${meta.id}" + + def index = args3.contains('--csi') ? 'csi' : 'tbi' """ mkdir ${prefix}_paraphase_vcfs touch ${prefix}.paraphase.json touch ${prefix}.paraphase.bam touch ${prefix}.paraphase.bam.bai - touch ${prefix}_paraphase_vcfs/${prefix}_stub.vcf + echo '' | gzip > ${prefix}_paraphase_vcfs/${prefix}_stub.vcf.gz + touch ${prefix}_paraphase_vcfs/${prefix}_stub.vcf.gz.${index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/paraphase/meta.yml b/modules/nf-core/paraphase/meta.yml index 4dae0dd8b4b2..e6cc6d635780 100644 --- a/modules/nf-core/paraphase/meta.yml +++ b/modules/nf-core/paraphase/meta.yml @@ -74,8 +74,12 @@ output: pattern: "*.paraphase.json" - vcf: type: file - description: VCF file(s) per gene - pattern: "*.vcf" + description: compressed VCF file(s) per gene + pattern: "*.vcf.gz" + - vcf_index: + type: file + description: compressed VCF file index + pattern: "*.vcf.gz.{tbi,csi}" authors: - "@fellen31" diff --git a/modules/nf-core/paraphase/tests/main.nf.test b/modules/nf-core/paraphase/tests/main.nf.test index ff35588f932a..e34d66991477 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test +++ b/modules/nf-core/paraphase/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process PARAPHASE" script "../main.nf" process "PARAPHASE" - config "./nextflow.config" tag "modules" tag "modules_nfcore" @@ -25,6 +24,9 @@ nextflow_process { } test("homo_sapiens - [ bam, bai ], []") { + + config "./nextflow.config" + when { process { """ @@ -45,16 +47,16 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert process.out.vcf_index.get(0).get(1).endsWith("tbi") }, { assert snapshot( file(process.out.json.get(0).get(1)).readLines()[0..39], - process.out.versions, - file(process.out.vcf.get(0).get(1)).readLines()[0..962], - process.out.bam ==~ "test.paraphase.bam", - process.out.bai ==~ "test.paraphase.bam.bai", + path(process.out.vcf.get(0).get(1)).linesGzip[10], + bam(process.out.bam.get(0).get(1)).getReadsMD5(), + file(process.out.bai.get(0).get(1)).name, + file(process.out.vcf_index.get(0).get(1)).name, + process.out.versions ).match() - }, - { assert process.out.bam.get(0).get(1) =~ "test.paraphase.bam" }, - { assert process.out.bai.get(0).get(1) =~ "test.paraphase.bam.bai" }, + } ) } @@ -62,6 +64,46 @@ nextflow_process { test("homo_sapiens - [ bam, bai ], config") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true), + ] + input[1] = TABIX_BGZIP.out.output + input[2] = [ + [ id:'test_config' ], + file(params.modules_testdata_base_path + 'generic/config/paraphase_config.yaml', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf_index.get(0).get(1).endsWith("tbi") }, + { assert snapshot( + file(process.out.json.get(0).get(1)).readLines()[0..39], + path(process.out.vcf.get(0).get(1)).linesGzip[10], + bam(process.out.bam.get(0).get(1)).getReadsMD5(), + file(process.out.bai.get(0).get(1)).name, + file(process.out.vcf_index.get(0).get(1)).name, + process.out.versions + ).match() + } + ) + } + } + + test("homo_sapiens - [ bam, bai ], config - csi_index") { + + config "./nextflow.csi_index.config" + when { process { """ @@ -82,16 +124,16 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert process.out.vcf_index.get(0).get(1).endsWith("csi") }, { assert snapshot( file(process.out.json.get(0).get(1)).readLines()[0..39], - process.out.versions, - file(process.out.vcf.get(0).get(1)).readLines()[0..962], - process.out.bam ==~ "test.paraphase.bam", - process.out.bai ==~ "test.paraphase.bam.bai", + path(process.out.vcf.get(0).get(1)).linesGzip[10], + bam(process.out.bam.get(0).get(1)).getReadsMD5(), + file(process.out.bai.get(0).get(1)).name, + file(process.out.vcf_index.get(0).get(1)).name, + process.out.versions ).match() - }, - { assert process.out.bam.get(0).get(1) =~ "test.paraphase.bam" }, - { assert process.out.bai.get(0).get(1) =~ "test.paraphase.bam.bai" }, + } ) } } @@ -99,6 +141,7 @@ nextflow_process { test("homo_sapiens - [ bam, bai ], [] - stub") { options "-stub" + config "./nextflow.config" when { process { @@ -128,6 +171,37 @@ nextflow_process { test("homo_sapiens - [ bam, bai ], config - stub") { options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true), + ] + input[1] = TABIX_BGZIP.out.output + input[2] = [ + [ id:'test_config' ], + file(params.modules_testdata_base_path + 'generic/config/paraphase_config.yaml', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - [ bam, bai ], config - stub - csi_index") { + + options "-stub" + config "./nextflow.csi_index.config" when { process { diff --git a/modules/nf-core/paraphase/tests/main.nf.test.snap b/modules/nf-core/paraphase/tests/main.nf.test.snap index 32242c1ca13a..b80a34434a61 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test.snap +++ b/modules/nf-core/paraphase/tests/main.nf.test.snap @@ -43,982 +43,19 @@ " \"unique_supporting_reads\": {", " \"12222212222111211221\": [" ], + "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", + "add24d02bf7f37b3ca30771c44ab4ee2", + "test.paraphase.bam.bai", + "test_PRODH.vcf.gz.tbi", [ "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" - ], - [ - "##fileformat=VCFv4.2", - "##FILTER=", - "##INFO=", - "##FORMAT=", - "##FORMAT=", - "##FORMAT=", - "##contig=", - "##paraphase_version=3.1.1", - "##paraphase_command=paraphase --gene PRODH --threads 2 --bam test.sorted.bam --reference test_ref.fa --prefix test --out .", - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tPRODH_hap1\tPRODH_hap2", - "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", - "chr22\t18912285\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912286\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912287\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912288\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912289\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912290\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912291\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912292\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912293\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912294\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:6:0,6", - "chr22\t18912295\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:3:0,3", - "chr22\t18912296\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912297\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912298\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912299\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:5:0,5\t.:3:0,1", - "chr22\t18912300\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912301\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912302\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912303\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:7:0,7", - "chr22\t18912304\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912305\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912306\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912307\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912308\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912309\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912310\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,9\t1:7:0,7", - "chr22\t18912311\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,7\t.:3:0,3", - "chr22\t18912312\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912313\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912314\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912315\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5", - "chr22\t18912316\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:6:0,4", - "chr22\t18912317\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912318\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912319\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912320\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912321\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912322\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912323\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912324\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912325\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - 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"chr22\t18912353\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:2:0,2", - "chr22\t18912354\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912355\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912356\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912357\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912358\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912359\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912360\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912361\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912362\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912363\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912364\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912365\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912366\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912367\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912368\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912369\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912370\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912371\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912372\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912373\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912374\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912375\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912376\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912377\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7", - "chr22\t18912378\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912379\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912380\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,4", - "chr22\t18912381\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912382\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5", - "chr22\t18912383\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912384\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912385\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912386\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912387\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912388\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912389\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912390\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912391\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912392\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912393\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912394\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912395\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912396\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912397\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912398\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912399\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912400\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912401\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912402\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912403\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912404\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912405\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912406\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - 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"chr22\t18912470\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912471\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912472\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912473\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912474\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912475\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912476\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912477\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912478\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912479\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912480\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912481\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912482\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912483\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912484\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912485\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912486\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912487\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912488\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912489\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912490\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912491\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912492\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912493\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912494\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912495\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912496\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - 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"chr22\t18912569\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912570\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912571\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912572\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4", - "chr22\t18912573\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3", - "chr22\t18912574\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912575\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912576\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4", - "chr22\t18912577\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912578\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912579\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912580\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912581\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912582\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912583\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912584\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912585\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912586\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912587\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912588\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912589\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912590\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912591\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912592\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912593\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912594\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912595\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - 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"chr22\t18912677\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912678\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912679\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912680\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912681\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912682\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912683\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912684\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912685\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - 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"chr22\t18912767\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912768\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912769\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912770\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3", - "chr22\t18912771\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912772\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912773\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912774\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912775\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912776\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7", - "chr22\t18912777\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912778\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912779\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912780\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912781\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912782\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912783\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912784\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - 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"chr22\t18912794\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912795\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912796\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912797\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912798\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912799\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912800\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912801\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912802\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - 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"chr22\t18912848\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912849\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912850\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912851\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912852\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912853\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912854\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912855\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912856\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912857\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912858\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912859\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912860\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912861\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912862\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912863\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912864\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912865\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912866\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912867\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3", - "chr22\t18912868\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912869\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912870\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912871\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912872\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912873\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912874\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912875\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912876\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912877\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912878\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912879\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912880\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912881\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4", - "chr22\t18912882\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912883\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912884\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912885\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912886\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912887\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912888\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912889\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912890\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912891\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912892\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912893\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912894\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912895\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912896\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18912897\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912898\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912899\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912900\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912901\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912902\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912903\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,2", - "chr22\t18912904\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912905\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912906\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912907\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912908\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912909\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912910\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - 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"chr22\t18912947\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912948\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912949\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912950\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912951\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912952\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912953\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:6:0,6", - "chr22\t18912954\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:4:0,4", - "chr22\t18912955\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912956\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912957\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912958\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912959\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912960\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912961\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912962\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912963\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912964\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912965\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912966\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7", - "chr22\t18912967\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912968\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912969\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912970\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912971\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912972\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912973\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912974\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912975\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912976\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912977\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912978\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912979\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912980\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912981\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912982\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912983\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912984\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912985\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912986\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912987\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912988\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912989\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912990\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912991\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912992\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912993\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912994\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912995\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4", - "chr22\t18912996\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912997\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912998\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912999\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913000\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18913001\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913002\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913003\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913004\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913005\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913006\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913007\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913008\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913009\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3", - 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"chr22\t18913037\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913038\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913039\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913040\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913041\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913042\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913043\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913044\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913045\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913046\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913047\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913048\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913049\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913050\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913051\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913052\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913053\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913054\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913055\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913056\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913057\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913058\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913059\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913060\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913061\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913062\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913063\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913064\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913065\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18913066\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913067\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913068\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18913069\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2", - "chr22\t18913070\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913071\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913072\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913073\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18913074\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913075\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913076\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913077\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913078\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913079\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913080\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913081\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913082\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913083\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913084\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913085\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913086\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913087\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913088\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913089\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913090\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913091\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913092\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913093\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913094\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913095\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913096\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913097\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913098\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913099\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - 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"chr22\t18913145\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913146\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913147\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913148\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913149\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913150\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913151\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913152\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913153\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - 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"chr22\t18913163\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913164\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913165\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913166\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913167\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913168\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913169\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913170\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913171\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913172\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913173\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913174\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913175\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913176\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913177\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913178\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913179\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913180\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913181\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913182\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913183\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913184\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913185\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913186\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913187\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913188\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913189\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913190\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913191\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913192\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913193\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913194\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18913195\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913196\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913197\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913198\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - 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"chr22\t18913217\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913218\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913219\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913220\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913221\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913222\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913223\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913224\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913225\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913226\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913227\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913228\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913229\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913230\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913231\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913232\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913233\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913234\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913235\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913236\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5" - ], - false, - false + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-29T15:14:21.054789211" + "timestamp": "2024-09-06T06:20:55.135067843" }, "homo_sapiens - [ bam, bai ], config - stub": { "content": [ @@ -1056,10 +93,19 @@ "id": "test", "single_end": true }, - "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" ], "bai": [ @@ -1095,7 +141,16 @@ "id": "test", "single_end": true }, - "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_index": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -1105,9 +160,67 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-29T17:44:03.275093922" + "timestamp": "2024-09-03T12:04:30.019868621" + }, + "homo_sapiens - [ bam, bai ], config - csi_index": { + "content": [ + [ + "{", + " \"PRODH\": {", + " \"total_cn\": 2,", + " \"gene_cn\": null,", + " \"final_haplotypes\": {", + " \"12222212222111211221\": \"PRODH_hap1\",", + " \"21111121111222122112\": \"PRODH_hap2\"", + " },", + " \"two_copy_haplotypes\": [],", + " \"alleles_final\": [],", + " \"hap_links\": {},", + " \"highest_total_cn\": 2,", + " \"assembled_haplotypes\": [", + " \"12222212222111211221\",", + " \"21111121111222122112\"", + " ],", + " \"sites_for_phasing\": [", + " \"18913237_G_A\",", + " \"18917224_G_A\",", + " \"18917246_A_C\",", + " \"18917262_G_A\",", + " \"18917266_T_C\",", + " \"18917362_C_A\",", + " \"18918010_C_T\",", + " \"18918465_G_A\",", + " \"18918847_T_C\",", + " \"18919892_G_T\",", + " \"18920342_G_A\",", + " \"18920484_C_T\",", + " \"18921128_C_T\",", + " \"18921213_T_C\",", + " \"18921638_T_G\",", + " \"18921763_T_C\",", + " \"18922744_C_T\",", + " \"18923032_C_T\",", + " \"18923315_T_G\",", + " \"18923644_G_A\"", + " ],", + " \"unique_supporting_reads\": {", + " \"12222212222111211221\": [" + ], + "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", + "add24d02bf7f37b3ca30771c44ab4ee2", + "test.paraphase.bam.bai", + "test_PRODH.vcf.gz.csi", + [ + "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T06:24:48.142490096" }, "homo_sapiens - [ bam, bai ], [] - stub": { "content": [ @@ -1145,10 +258,19 @@ "id": "test", "single_end": true }, - "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" ], "bai": [ @@ -1184,7 +306,16 @@ "id": "test", "single_end": true }, - "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_index": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -1194,9 +325,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-29T17:43:56.008820548" + "timestamp": "2024-09-03T12:04:14.370756094" }, "homo_sapiens - [ bam, bai ], config": { "content": [ @@ -1242,981 +373,125 @@ " \"unique_supporting_reads\": {", " \"12222212222111211221\": [" ], + "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", + "add24d02bf7f37b3ca30771c44ab4ee2", + "test.paraphase.bam.bai", + "test_PRODH.vcf.gz.tbi", [ "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" - ], - [ - "##fileformat=VCFv4.2", - "##FILTER=", - "##INFO=", - "##FORMAT=", - "##FORMAT=", - "##FORMAT=", - "##contig=", - "##paraphase_version=3.1.1", - "##paraphase_command=paraphase --gene PRODH --threads 2 --bam test.sorted.bam --reference test_ref.fa --prefix test --config paraphase_config.yaml --out .", - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tPRODH_hap1\tPRODH_hap2", - "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", - "chr22\t18912285\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912286\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912287\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912288\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912289\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912290\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912291\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912292\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912293\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912294\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:6:0,6", - "chr22\t18912295\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:3:0,3", - "chr22\t18912296\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912297\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912298\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912299\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:5:0,5\t.:3:0,1", - "chr22\t18912300\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912301\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912302\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912303\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:7:0,7", - "chr22\t18912304\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912305\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912306\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912307\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912308\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912309\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912310\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,9\t1:7:0,7", - "chr22\t18912311\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,7\t.:3:0,3", - "chr22\t18912312\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912313\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912314\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912315\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5", - "chr22\t18912316\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:6:0,4", - "chr22\t18912317\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912318\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912319\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912320\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912321\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912322\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912323\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912324\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912325\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - 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"chr22\t18912353\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:2:0,2", - "chr22\t18912354\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912355\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912356\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912357\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912358\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912359\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912360\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912361\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912362\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912363\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912364\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912365\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912366\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912367\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912368\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912369\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912370\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912371\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912372\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912373\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912374\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912375\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912376\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912377\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7", - "chr22\t18912378\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912379\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912380\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,4", - "chr22\t18912381\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912382\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5", - "chr22\t18912383\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912384\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912385\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912386\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912387\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912388\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912389\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912390\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912391\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912392\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912393\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912394\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912395\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912396\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912397\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912398\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912399\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912400\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912401\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912402\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912403\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912404\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912405\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912406\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - 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"chr22\t18912470\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912471\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912472\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912473\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912474\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912475\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912476\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912477\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912478\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912479\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912480\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912481\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912482\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912483\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912484\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912485\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912486\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912487\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912488\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912489\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912490\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912491\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912492\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912493\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912494\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912495\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912496\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - 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"chr22\t18912569\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912570\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912571\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912572\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4", - "chr22\t18912573\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3", - "chr22\t18912574\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912575\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912576\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4", - "chr22\t18912577\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912578\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912579\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912580\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912581\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912582\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912583\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912584\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912585\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912586\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912587\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912588\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912589\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912590\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912591\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912592\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912593\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912594\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912595\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - 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"chr22\t18912677\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912678\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912679\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912680\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912681\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912682\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912683\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912684\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912685\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - 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"chr22\t18912767\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912768\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912769\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912770\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3", - "chr22\t18912771\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912772\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912773\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912774\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912775\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912776\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7", - "chr22\t18912777\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912778\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912779\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912780\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912781\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912782\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912783\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912784\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - 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"chr22\t18912794\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912795\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912796\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912797\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912798\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912799\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912800\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912801\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912802\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - 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"chr22\t18912848\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912849\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912850\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912851\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912852\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912853\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912854\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912855\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912856\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912857\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912858\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912859\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912860\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912861\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912862\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912863\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912864\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912865\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912866\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912867\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3", - "chr22\t18912868\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912869\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912870\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912871\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912872\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912873\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912874\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912875\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912876\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912877\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912878\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912879\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912880\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912881\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4", - "chr22\t18912882\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912883\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912884\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912885\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912886\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912887\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912888\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912889\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912890\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912891\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912892\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912893\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912894\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912895\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912896\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18912897\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912898\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912899\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912900\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912901\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912902\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912903\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,2", - "chr22\t18912904\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912905\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912906\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912907\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912908\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912909\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912910\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - 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"chr22\t18912947\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912948\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912949\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912950\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912951\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912952\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912953\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:6:0,6", - "chr22\t18912954\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:4:0,4", - "chr22\t18912955\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912956\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912957\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912958\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912959\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912960\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912961\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912962\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912963\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912964\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912965\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912966\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7", - "chr22\t18912967\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912968\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912969\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912970\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912971\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912972\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912973\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912974\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912975\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912976\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912977\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912978\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912979\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912980\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912981\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912982\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912983\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912984\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912985\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912986\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912987\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912988\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912989\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912990\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912991\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912992\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912993\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912994\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912995\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4", - "chr22\t18912996\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912997\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912998\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912999\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913000\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18913001\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913002\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913003\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913004\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913005\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913006\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913007\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913008\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913009\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3", - 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"chr22\t18913037\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913038\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913039\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913040\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913041\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913042\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913043\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913044\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913045\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913046\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913047\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913048\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913049\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913050\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913051\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913052\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913053\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913054\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913055\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913056\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913057\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913058\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913059\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913060\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913061\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913062\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913063\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913064\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913065\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18913066\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913067\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913068\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18913069\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2", - "chr22\t18913070\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913071\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913072\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913073\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18913074\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913075\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913076\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913077\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913078\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913079\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913080\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913081\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913082\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913083\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913084\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913085\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913086\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913087\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913088\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913089\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913090\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913091\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913092\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913093\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913094\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913095\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913096\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913097\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913098\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913099\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - 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"chr22\t18913145\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913146\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913147\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913148\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913149\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913150\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913151\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913152\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913153\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - 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"chr22\t18913163\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913164\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913165\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913166\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913167\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913168\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913169\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913170\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913171\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913172\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913173\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913174\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913175\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913176\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913177\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913178\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913179\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913180\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913181\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913182\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913183\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913184\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913185\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913186\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913187\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913188\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913189\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913190\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913191\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913192\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913193\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913194\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18913195\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913196\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913197\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913198\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913199\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913200\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913201\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913202\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913203\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18913204\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5", - "chr22\t18913205\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913206\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913207\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18913208\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913209\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913210\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913211\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913212\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913213\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913214\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913215\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913216\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913217\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913218\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913219\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913220\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913221\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913222\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913223\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913224\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913225\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913226\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913227\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913228\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913229\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913230\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913231\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913232\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913233\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913234\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913235\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913236\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5" - ], - false, - false + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T06:24:34.443854854" + }, + "homo_sapiens - [ bam, bai ], config - stub - csi_index": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" + ], + "bai": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "json": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_index": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" + ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-29T15:14:33.451355236" + "timestamp": "2024-09-03T12:10:23.256066977" } } \ No newline at end of file diff --git a/modules/nf-core/paraphase/tests/nextflow.csi_index.config b/modules/nf-core/paraphase/tests/nextflow.csi_index.config new file mode 100644 index 000000000000..df8ee6c39bca --- /dev/null +++ b/modules/nf-core/paraphase/tests/nextflow.csi_index.config @@ -0,0 +1,6 @@ +process { + withName: 'PARAPHASE' { + ext.args = '--gene PRODH' + ext.args3 = '--csi' + } +} diff --git a/modules/nf-core/purecn/intervalfile/environment.yml b/modules/nf-core/purecn/intervalfile/environment.yml index 6caebe5ad3d9..1597c765c500 100644 --- a/modules/nf-core/purecn/intervalfile/environment.yml +++ b/modules/nf-core/purecn/intervalfile/environment.yml @@ -1,10 +1,14 @@ name: purecn_intervalfile + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::bioconductor-purecn=2.4.0 - - bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.16.0 - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2 - - bioconda::bioconductor-org.hs.eg.db=3.16.0 + - bioconda::bioconductor-org.hs.eg.db=3.18.0 + - bioconda::bioconductor-purecn=2.8.1 + - bioconda::bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2 + - bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.18.0 + - conda-forge::r-optparse=1.7.5 + - conda-forge::r-r.utils=2.12.3 diff --git a/modules/nf-core/purecn/intervalfile/main.nf b/modules/nf-core/purecn/intervalfile/main.nf index b8d4c69feab7..49434776d0c6 100644 --- a/modules/nf-core/purecn/intervalfile/main.nf +++ b/modules/nf-core/purecn/intervalfile/main.nf @@ -2,11 +2,10 @@ process PURECN_INTERVALFILE { tag "${meta.id}" label 'process_low' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-582ac26068889091d5e798347c637f8208d77a71:a29c64a63498b1ee8b192521fdf6ed3c65506994-0': - 'biocontainers/mulled-v2-582ac26068889091d5e798347c637f8208d77a71:a29c64a63498b1ee8b192521fdf6ed3c65506994-0' }" + 'oras://community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:c04754ed02eb7cd3': + 'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:cd51f6d3c90eb24f' }" input: tuple val(meta), path(target_bed) @@ -25,7 +24,6 @@ process PURECN_INTERVALFILE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '2.4.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ library_path=\$(Rscript -e 'cat(.libPaths(), sep = "\\n")') @@ -38,7 +36,7 @@ process PURECN_INTERVALFILE { cat <<-END_VERSIONS > versions.yml "${task.process}": - purecn: ${VERSION} + purecn: \$(Rscript -e 'packageVersion("PureCN")' | sed -n 's|\\[1\\] ‘\\(.*\\)’|\\1|p') END_VERSIONS """ @@ -47,14 +45,13 @@ process PURECN_INTERVALFILE { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def bed = args.contains("--export") ? "touch ${prefix}.bed" : "" - def VERSION = '2.4.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}.txt ${bed} cat <<-END_VERSIONS > versions.yml "${task.process}": - purecn: ${VERSION} + purecn: \$(Rscript -e 'packageVersion("PureCN")' | sed -n 's|\\[1\\] ‘\\(.*\\)’|\\1|p') END_VERSIONS """ } diff --git a/modules/nf-core/purecn/intervalfile/meta.yml b/modules/nf-core/purecn/intervalfile/meta.yml index 51f5b3a6b7b5..489fed1cd073 100644 --- a/modules/nf-core/purecn/intervalfile/meta.yml +++ b/modules/nf-core/purecn/intervalfile/meta.yml @@ -13,8 +13,7 @@ tools: documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z." - licence: "Artistic-2.0" - args_id: "$args" + licence: ["Artistic-2.0"] input: - meta: type: map diff --git a/modules/nf-core/purecn/intervalfile/tests/main.nf.test b/modules/nf-core/purecn/intervalfile/tests/main.nf.test new file mode 100644 index 000000000000..a14a0cbb4501 --- /dev/null +++ b/modules/nf-core/purecn/intervalfile/tests/main.nf.test @@ -0,0 +1,60 @@ + +nextflow_process { + + name "Test Process PURECN_INTERVALFILE" + script "../main.nf" + process "PURECN_INTERVALFILE" + + tag "modules" + tag "modules_nfcore" + tag "purecn" + tag "purecn/intervalfile" + + test("test-purecn-intervalfile") { + + when { + process { + """ + input[0] = [[id: "test"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)] + input[1] = [[id: "fasta"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)] + input[2] = "hg38" + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.txt[0][1]).readLines()[3..7], + process.out.bed, + process.out.versions + ).match() + } + ) + } + } + + test("test-purecn-intervalfile-stub") { + options '-stub' + when { + process { + """ + input[0] = [[id: "test"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)] + input[1] = [[id: "fasta"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)] + input[2] = "hg38" + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/purecn/intervalfile/tests/main.nf.test.snap b/modules/nf-core/purecn/intervalfile/tests/main.nf.test.snap new file mode 100644 index 000000000000..fd2ed40e66a0 --- /dev/null +++ b/modules/nf-core/purecn/intervalfile/tests/main.nf.test.snap @@ -0,0 +1,63 @@ +{ + "test-purecn-intervalfile-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,1f04b2a85be5b27512547a3d0ebfcd79" + ], + "bed": [ + + ], + "txt": [ + [ + { + "id": "test" + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1f04b2a85be5b27512547a3d0ebfcd79" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T16:05:41.414832" + }, + "test-purecn-intervalfile": { + "content": [ + [ + "chr21:5010001-5010400\t0.5325\tNA\tNA\t.\tTRUE", + "chr21:5010401-5010800\t0.4625\tNA\tNA\t.\tTRUE", + "chr21:5010801-5011200\t0.55\tNA\tNA\t.\tTRUE", + "chr21:5011201-5011600\t0.425\tNA\tNA\t.\tTRUE", + "chr21:5011601-5012000\t0.6275\tNA\tNA\t.\tTRUE" + ], + [ + + ], + [ + "versions.yml:md5,1f04b2a85be5b27512547a3d0ebfcd79" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T16:05:20.272038" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index ccdc7efec935..7eb658fe5cc1 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -43,18 +43,12 @@ bbmap/align: bcftools/convert: - modules/nf-core/bcftools/convert/** - tests/modules/nf-core/bcftools/convert/** -bcftools/merge: - - modules/nf-core/bcftools/merge/** - - tests/modules/nf-core/bcftools/merge/** bedtools/intersect: - modules/nf-core/bedtools/intersect/** - tests/modules/nf-core/bedtools/intersect/** bedtools/unionbedg: - modules/nf-core/bedtools/unionbedg/** - tests/modules/nf-core/bedtools/unionbedg/** -biobambam/bamsormadup: - - modules/nf-core/biobambam/bamsormadup/** - - tests/modules/nf-core/biobambam/bamsormadup/** biohansel: - modules/nf-core/biohansel/** - tests/modules/nf-core/biohansel/** @@ -94,15 +88,9 @@ cellrangeratac/mkref: checkm/qa: - modules/nf-core/checkm/qa/** - tests/modules/nf-core/checkm/qa/** -circexplorer2/parse: - - modules/nf-core/circexplorer2/parse/** - - tests/modules/nf-core/circexplorer2/parse/** clippy: - modules/nf-core/clippy/** - tests/modules/nf-core/clippy/** -cnvkit/call: - - modules/nf-core/cnvkit/call/** - - tests/modules/nf-core/cnvkit/call/** cnvkit/export: - modules/nf-core/cnvkit/export/** - tests/modules/nf-core/cnvkit/export/** @@ -175,9 +163,6 @@ elprep/filter: elprep/merge: - modules/nf-core/elprep/merge/** - tests/modules/nf-core/elprep/merge/** -emboss/revseq: - - modules/nf-core/emboss/revseq/** - - tests/modules/nf-core/emboss/revseq/** emboss/seqret: - modules/nf-core/emboss/seqret/** - tests/modules/nf-core/emboss/seqret/** @@ -278,12 +263,6 @@ genotyphi/parse: genrich: - modules/nf-core/genrich/** - tests/modules/nf-core/genrich/** -geoquery/getgeo: - - modules/nf-core/geoquery/getgeo/** - - tests/modules/nf-core/geoquery/getgeo/** -gfaffix: - - modules/nf-core/gfaffix/** - - tests/modules/nf-core/gfaffix/** gfastats: - modules/nf-core/gfastats/** - tests/modules/nf-core/gfastats/** @@ -296,9 +275,6 @@ glimpse2/concordance: glnexus: - modules/nf-core/glnexus/** - tests/modules/nf-core/glnexus/** -goleft/indexsplit: - - modules/nf-core/goleft/indexsplit/** - - tests/modules/nf-core/goleft/indexsplit/** gprofiler2/gost: - modules/nf-core/gprofiler2/gost/** - tests/modules/nf-core/gprofiler2/gost/** @@ -308,9 +284,6 @@ graphmap2/align: graphtyper/genotype: - modules/nf-core/graphtyper/genotype/** - tests/modules/nf-core/graphtyper/genotype/** -graphtyper/vcfconcatenate: - - modules/nf-core/graphtyper/vcfconcatenate/** - - tests/modules/nf-core/graphtyper/vcfconcatenate/** grids/gridsssomaticfilter: - modules/nf-core/grids/gridsssomaticfilter/** - tests/modules/nf-core/grids/gridsssomaticfilter/** @@ -320,9 +293,6 @@ gridss/gridssgenerateponbedpe: gsea/gsea: - modules/nf-core/gsea/gsea/** - tests/modules/nf-core/gsea/gsea/** -gubbins: - - modules/nf-core/gubbins/** - - tests/modules/nf-core/gubbins/** gunc/downloaddb: - modules/nf-core/gunc/downloaddb/** - tests/modules/nf-core/gunc/downloaddb/** @@ -332,12 +302,6 @@ gunc/mergecheckm: gunc/run: - modules/nf-core/gunc/run/** - tests/modules/nf-core/gunc/run/** -hapibd: - - modules/nf-core/hapibd/** - - tests/modules/nf-core/hapibd/** -haplogrep2/classify: - - modules/nf-core/haplogrep2/classify/** - - tests/modules/nf-core/haplogrep2/classify/** hicexplorer/hicpca: - modules/nf-core/hicexplorer/hicpca/** - tests/modules/nf-core/hicexplorer/hicpca/** @@ -359,24 +323,12 @@ hmmer/eslreformat: hmmer/hmmalign: - modules/nf-core/hmmer/hmmalign/** - tests/modules/nf-core/hmmer/hmmalign/** -hmmer/hmmbuild: - - modules/nf-core/hmmer/hmmbuild/** - - tests/modules/nf-core/hmmer/hmmbuild/** -hmmer/hmmfetch: - - modules/nf-core/hmmer/hmmfetch/** - - tests/modules/nf-core/hmmer/hmmfetch/** hmtnote/annotate: - modules/nf-core/hmtnote/annotate/** - tests/modules/nf-core/hmtnote/annotate/** -homer/annotatepeaks: - - modules/nf-core/homer/annotatepeaks/** - - tests/modules/nf-core/homer/annotatepeaks/** homer/makeucscfile: - modules/nf-core/homer/makeucscfile/** - tests/modules/nf-core/homer/makeucscfile/** -hypo: - - modules/nf-core/hypo/** - - tests/modules/nf-core/hypo/** icountmini/metagene: - modules/nf-core/icountmini/metagene/** - tests/modules/nf-core/icountmini/metagene/** @@ -389,9 +341,6 @@ icountmini/sigxls: icountmini/summary: - modules/nf-core/icountmini/summary/** - tests/modules/nf-core/icountmini/summary/** -idr: - - modules/nf-core/idr/** - - tests/modules/nf-core/idr/** ilastik/multicut: - modules/nf-core/ilastik/multicut/** - tests/modules/nf-core/ilastik/multicut/** @@ -410,9 +359,6 @@ iphop/predict: ivar/consensus: - modules/nf-core/ivar/consensus/** - tests/modules/nf-core/ivar/consensus/** -ivar/variants: - - modules/nf-core/ivar/variants/** - - tests/modules/nf-core/ivar/variants/** jupyternotebook: - modules/nf-core/jupyternotebook/** - tests/modules/nf-core/jupyternotebook/** @@ -452,15 +398,9 @@ krona/ktimporttext: leehom: - modules/nf-core/leehom/** - tests/modules/nf-core/leehom/** -legsta: - - modules/nf-core/legsta/** - - tests/modules/nf-core/legsta/** limma/differential: - modules/nf-core/limma/differential/** - tests/modules/nf-core/limma/differential/** -mapdamage2: - - modules/nf-core/mapdamage2/** - - tests/modules/nf-core/mapdamage2/** maxquant/lfq: - modules/nf-core/maxquant/lfq/** - tests/modules/nf-core/maxquant/lfq/** @@ -506,9 +446,6 @@ mitohifi/mitohifi: mmseqs/cluster: - modules/nf-core/mmseqs/cluster/** - tests/modules/nf-core/mmseqs/cluster/** -mmseqs/databases: - - modules/nf-core/mmseqs/databases/** - - tests/modules/nf-core/mmseqs/databases/** mmseqs/easysearch: - modules/nf-core/mmseqs/easysearch/** - tests/modules/nf-core/mmseqs/easysearch/** @@ -632,9 +569,6 @@ proteus/readproteingroups: purecn/coverage: - modules/nf-core/purecn/coverage/** - tests/modules/nf-core/purecn/coverage/** -purecn/intervalfile: - - modules/nf-core/purecn/intervalfile/** - - tests/modules/nf-core/purecn/intervalfile/** purecn/run: - modules/nf-core/purecn/run/** - tests/modules/nf-core/purecn/run/** diff --git a/tests/modules/nf-core/bcftools/merge/main.nf b/tests/modules/nf-core/bcftools/merge/main.nf deleted file mode 100644 index af1060bdd5f2..000000000000 --- a/tests/modules/nf-core/bcftools/merge/main.nf +++ /dev/null @@ -1,71 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -//keep --no-verson argument, otherwise md5 will change on each execution -include { BCFTOOLS_MERGE } from '../../../../../modules/nf-core/bcftools/merge/main.nf' -include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_GVCF } from '../../../../../modules/nf-core/bcftools/merge/main.nf' -include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_BCF } from '../../../../../modules/nf-core/bcftools/merge/main.nf' - -workflow test_bcftools_merge { - input = [ [ id:'test' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ], - [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ] - ] - - bed = [] - fasta = [[],[]] - fai = [[],[]] - - BCFTOOLS_MERGE ( input, fasta, fai, bed ) -} - -workflow test_bcftools_merge_bed { - input = [ [ id:'test' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ], - [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ] - ] - - bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - fasta = [[],[]] - fai = [[],[]] - - BCFTOOLS_MERGE ( input, fasta, fai, bed ) -} - -workflow test_bcftools_merge_gvcf { - input = [ [ id:'test' ], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true) ], - [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz_tbi'], checkIfExists: true) ] - ] - - bed = [] - fasta = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - fai = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - BCFTOOLS_MERGE_GVCF ( input, fasta, fai, bed ) -} - -workflow test_bcftools_merge_bcf { - input = [ [ id:'test' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ], - [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ] - ] - - bed = [] - fasta = [[],[]] - fai = [[],[]] - - BCFTOOLS_MERGE_BCF ( input, fasta, fai, bed ) -} diff --git a/tests/modules/nf-core/bcftools/merge/nextflow.config b/tests/modules/nf-core/bcftools/merge/nextflow.config deleted file mode 100644 index c2b7972f07e0..000000000000 --- a/tests/modules/nf-core/bcftools/merge/nextflow.config +++ /dev/null @@ -1,17 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: BCFTOOLS_MERGE { - ext.args = '--force-samples --no-version --output-type z' - } - - withName: BCFTOOLS_MERGE_GVCF { - ext.args = {"--force-samples --no-version -m none --output-type z --gvcf $fasta"} - } - - withName: BCFTOOLS_MERGE_BCF { - ext.args = "--force-samples --no-version --output-type b" - } - -} diff --git a/tests/modules/nf-core/bcftools/merge/test.yml b/tests/modules/nf-core/bcftools/merge/test.yml deleted file mode 100644 index c5751a91e848..000000000000 --- a/tests/modules/nf-core/bcftools/merge/test.yml +++ /dev/null @@ -1,63 +0,0 @@ -- name: bcftools merge test_bcftools_merge - command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config - tags: - - bcftools/merge - - bcftools - files: - - path: output/bcftools/test.vcf.gz - -- name: bcftools merge test_bcftools_merge_stub - command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config -stub-run - tags: - - bcftools/merge - - bcftools - files: - - path: output/bcftools/test.vcf.gz - -- name: bcftools merge test_bcftools_merge_bed - command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config - tags: - - bcftools/merge - - bcftools - files: - - path: output/bcftools/test.vcf.gz - -- name: bcftools merge test_bcftools_merge_bed_stub - command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config -stub-run - tags: - - bcftools/merge - - bcftools - files: - - path: output/bcftools/test.vcf.gz - -- name: bcftools merge test_bcftools_merge_gvcf - command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config - tags: - - bcftools/merge - - bcftools - files: - - path: output/bcftools/test.vcf.gz - -- name: bcftools merge test_bcftools_merge_gvcf_stub - command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config -stub-run - tags: - - bcftools/merge - - bcftools - files: - - path: output/bcftools/test.vcf.gz - -- name: bcftools merge test_bcftools_merge_bcf - command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_bcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config - tags: - - bcftools/merge - - bcftools - files: - - path: output/bcftools/test.bcf.gz - -- name: bcftools merge test_bcftools_merge_bcf_stub - command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_bcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config -stub-run - tags: - - bcftools/merge - - bcftools - files: - - path: output/bcftools/test.bcf.gz diff --git a/tests/modules/nf-core/biobambam/bamsormadup/main.nf b/tests/modules/nf-core/biobambam/bamsormadup/main.nf deleted file mode 100644 index b00cd505a71e..000000000000 --- a/tests/modules/nf-core/biobambam/bamsormadup/main.nf +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BIOBAMBAM_BAMSORMADUP } from '../../../../../modules/nf-core/biobambam/bamsormadup/main.nf' - -workflow test_biobambam_bamsormadup_multi_input { - - input = [ - [ id:'test', single_end:false ], // meta map - [file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)], - ] - - BIOBAMBAM_BAMSORMADUP ( input, [[:],[]] ) -} - -workflow test_biobambam_bamsormadup_single_input { - - input = [ - [ id:'test', single_end:false ], // meta map - [file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)], - ] - - BIOBAMBAM_BAMSORMADUP ( input, [[:],[]] ) -} diff --git a/tests/modules/nf-core/biobambam/bamsormadup/nextflow.config b/tests/modules/nf-core/biobambam/bamsormadup/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/biobambam/bamsormadup/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/biobambam/bamsormadup/test.yml b/tests/modules/nf-core/biobambam/bamsormadup/test.yml deleted file mode 100644 index 69808d797f6a..000000000000 --- a/tests/modules/nf-core/biobambam/bamsormadup/test.yml +++ /dev/null @@ -1,23 +0,0 @@ -- name: biobambam bamsormadup test_biobambam_bamsormadup_multi_input - command: nextflow run ./tests/modules/nf-core/biobambam/bamsormadup -entry test_biobambam_bamsormadup_multi_input -c ./tests/config/nextflow.config - tags: - - biobambam/bamsormadup - - biobambam - files: - - path: output/biobambam/test.bam - md5sum: 532b96d9826bc9b01973e49cc4bb316f - - path: output/biobambam/test.metrics.txt - md5sum: 020be21f1b7da0dca721a41e22d7ee02 - - path: output/biobambam/versions.yml - -- name: biobambam bamsormadup test_biobambam_bamsormadup_single_input - command: nextflow run ./tests/modules/nf-core/biobambam/bamsormadup -entry test_biobambam_bamsormadup_single_input -c ./tests/config/nextflow.config - tags: - - biobambam/bamsormadup - - biobambam - files: - - path: output/biobambam/test.bam - md5sum: 238f20beb8f62763e35cb96f311c8f04 - - path: output/biobambam/test.metrics.txt - md5sum: b97458eff0d4b259055e4902849ee53b - - path: output/biobambam/versions.yml diff --git a/tests/modules/nf-core/circexplorer2/parse/main.nf b/tests/modules/nf-core/circexplorer2/parse/main.nf deleted file mode 100644 index 52918ea39cc0..000000000000 --- a/tests/modules/nf-core/circexplorer2/parse/main.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { CIRCEXPLORER2_PARSE } from '../../../../../modules/nf-core/circexplorer2/parse/main.nf' - -workflow test_circexplorer2_parse { - - input = [ - [ id:'fust1_3' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction") - ] - - CIRCEXPLORER2_PARSE ( input ) - -} diff --git a/tests/modules/nf-core/circexplorer2/parse/nextflow.config b/tests/modules/nf-core/circexplorer2/parse/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/circexplorer2/parse/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/circexplorer2/parse/test.yml b/tests/modules/nf-core/circexplorer2/parse/test.yml deleted file mode 100644 index 0b7a4a2e7290..000000000000 --- a/tests/modules/nf-core/circexplorer2/parse/test.yml +++ /dev/null @@ -1,16 +0,0 @@ -- name: circexplorer2 parse test_circexplorer2_parse - command: nextflow run ./tests/modules/nf-core/circexplorer2/parse -entry test_circexplorer2_parse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/circexplorer2/parse/nextflow.config - tags: - - circexplorer2/parse - - circexplorer2 - files: - - path: output/circexplorer2/fust1_3.bed - md5sum: 592e0594c4d588a055f36fb1c3d04729 - -- name: circexplorer2 parse test_circexplorer2_parse_stub - command: nextflow run ./tests/modules/nf-core/circexplorer2/parse -entry test_circexplorer2_parse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/circexplorer2/parse/nextflow.config -stub - tags: - - circexplorer2/parse - - circexplorer2 - files: - - path: output/circexplorer2/fust1_3.bed diff --git a/tests/modules/nf-core/cnvkit/call/main.nf b/tests/modules/nf-core/cnvkit/call/main.nf deleted file mode 100644 index 17a88db14776..000000000000 --- a/tests/modules/nf-core/cnvkit/call/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { CNVKIT_CALL } from '../../../../../modules/nf-core/cnvkit/call/main.nf' - -workflow test_cnvkit_call { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['cnvkit']['amplicon_cns'], checkIfExists: true), - [] - ] - - CNVKIT_CALL ( input ) -} - -workflow test_cnvkit_call_with_vcf { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['cnvkit']['amplicon_cns'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) - ] - - CNVKIT_CALL ( input ) -} \ No newline at end of file diff --git a/tests/modules/nf-core/cnvkit/call/nextflow.config b/tests/modules/nf-core/cnvkit/call/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/cnvkit/call/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/cnvkit/call/test.yml b/tests/modules/nf-core/cnvkit/call/test.yml deleted file mode 100644 index 261c77ae4c46..000000000000 --- a/tests/modules/nf-core/cnvkit/call/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: cnvkit call test_cnvkit_call - command: nextflow run ./tests/modules/nf-core/cnvkit/call -entry test_cnvkit_call -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/call/nextflow.config - tags: - - cnvkit/call - - cnvkit - files: - - path: output/cnvkit/test.cns - md5sum: 7746029caf9ecc134a075a2d50be269f - - path: output/cnvkit/versions.yml - -- name: cnvkit call test_cnvkit_call_with_vcf - command: nextflow run ./tests/modules/nf-core/cnvkit/call -entry test_cnvkit_call_with_vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/call/nextflow.config - tags: - - cnvkit/call - - cnvkit - files: - - path: output/cnvkit/test.cns - md5sum: 2a4b3da8a8131a4ed4ae902a9f96a405 - - path: output/cnvkit/versions.yml diff --git a/tests/modules/nf-core/emboss/revseq/main.nf b/tests/modules/nf-core/emboss/revseq/main.nf deleted file mode 100644 index f6a5cf1e684e..000000000000 --- a/tests/modules/nf-core/emboss/revseq/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { EMBOSS_REVSEQ } from '../../../../../modules/nf-core/emboss/revseq/main.nf' - -workflow test_emboss_revseq { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - EMBOSS_REVSEQ ( input ) -} diff --git a/tests/modules/nf-core/emboss/revseq/nextflow.config b/tests/modules/nf-core/emboss/revseq/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/emboss/revseq/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/emboss/revseq/test.yml b/tests/modules/nf-core/emboss/revseq/test.yml deleted file mode 100644 index 5cbc7e368f78..000000000000 --- a/tests/modules/nf-core/emboss/revseq/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: emboss revseq test_emboss_revseq - command: nextflow run ./tests/modules/nf-core/emboss/revseq -entry test_emboss_revseq -c ./tests/config/nextflow.config - tags: - - emboss/revseq - - emboss - files: - - path: output/emboss/test.rev.fasta - md5sum: 78a4b77f08b5c95ab24e592f543f679c - - path: output/emboss/versions.yml diff --git a/tests/modules/nf-core/geoquery/getgeo/main.nf b/tests/modules/nf-core/geoquery/getgeo/main.nf deleted file mode 100644 index 1f40aa6c5534..000000000000 --- a/tests/modules/nf-core/geoquery/getgeo/main.nf +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GEOQUERY_GETGEO } from '../../../../../modules/nf-core/geoquery/getgeo/main.nf' - -workflow test_geoquery_getgeo { - - input = [[ id:'test' ], // meta map - 'GSE50790' - ] - - GEOQUERY_GETGEO ( input ) -} - -workflow test_geoquery_getgeo_with_metacols { - - input = [[ id:'test' ], // meta map - 'GSE50790' - ] - - GEOQUERY_GETGEO ( input ) -} diff --git a/tests/modules/nf-core/geoquery/getgeo/nextflow.config b/tests/modules/nf-core/geoquery/getgeo/nextflow.config deleted file mode 100644 index a191b883efc4..000000000000 --- a/tests/modules/nf-core/geoquery/getgeo/nextflow.config +++ /dev/null @@ -1,10 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: 'test_geoquery_getgeo_with_metacols:GEOQUERY_GETGEO' { - ext.args = { "--metacols \"ID,ENTREZ_GENE_ID,Gene Symbol,Sequence Type\"" } - ext.prefix = { "${meta.id}." } - } - -} diff --git a/tests/modules/nf-core/geoquery/getgeo/test.yml b/tests/modules/nf-core/geoquery/getgeo/test.yml deleted file mode 100644 index 1f13db5c22de..000000000000 --- a/tests/modules/nf-core/geoquery/getgeo/test.yml +++ /dev/null @@ -1,25 +0,0 @@ -- name: geoquery getgeo test_geoquery_getgeo - command: nextflow run ./tests/modules/nf-core/geoquery/getgeo -entry test_geoquery_getgeo -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/geoquery/getgeo/nextflow.config - tags: - - geoquery/getgeo - - geoquery - files: - - path: output/geoquery/annotation.tsv - md5sum: 4dbb874b49a11dff13557f58da643ee0 - - path: output/geoquery/eset.rds - - path: output/geoquery/matrix.tsv - md5sum: 230f87f91c0c1a7e2ab354200c4b978c - - path: output/geoquery/versions.yml - -- name: geoquery getgeo test_geoquery_getgeo_with_metacols - command: nextflow run ./tests/modules/nf-core/geoquery/getgeo -entry test_geoquery_getgeo_with_metacols -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/geoquery/getgeo/nextflow.config - tags: - - geoquery/getgeo - - geoquery - files: - - path: output/geoquery/test.annotation.tsv - md5sum: 40300ae222ae35fa54daf10a1b86e830 - - path: output/geoquery/test.eset.rds - - path: output/geoquery/test.matrix.tsv - md5sum: 230f87f91c0c1a7e2ab354200c4b978c - - path: output/geoquery/versions.yml diff --git a/tests/modules/nf-core/gfaffix/main.nf b/tests/modules/nf-core/gfaffix/main.nf deleted file mode 100644 index 712f7dca3e16..000000000000 --- a/tests/modules/nf-core/gfaffix/main.nf +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GFAFFIX } from '../../../../modules/nf-core/gfaffix/main.nf' - -workflow test_gfaffix { - input = [ [ id:'test' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)] - ] - - GFAFFIX ( input ) -} diff --git a/tests/modules/nf-core/gfaffix/nextflow.config b/tests/modules/nf-core/gfaffix/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/gfaffix/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/gfaffix/test.yml b/tests/modules/nf-core/gfaffix/test.yml deleted file mode 100644 index 4c47c0ab78f0..000000000000 --- a/tests/modules/nf-core/gfaffix/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: gfaffix - command: nextflow run ./tests/modules/nf-core/gfaffix -entry test_gfaffix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gfaffix/nextflow.config - tags: - - gfaffix - files: - - path: output/gfaffix/test.gfaffix.gfa - md5sum: 30d7a68fc07623779dbb3d708320c844 - - path: output/gfaffix/test.affixes.txt - md5sum: c3540baa386462552d7ebe4e4b7eda6a diff --git a/tests/modules/nf-core/goleft/indexsplit/main.nf b/tests/modules/nf-core/goleft/indexsplit/main.nf deleted file mode 100644 index 30df3304d63f..000000000000 --- a/tests/modules/nf-core/goleft/indexsplit/main.nf +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GOLEFT_INDEXSPLIT } from '../../../../../modules/nf-core/goleft/indexsplit/main.nf' - -workflow test_goleft_indexsplit { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true) - ] - - fai = [ - [ id:'sarscov2'], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - - ] - - GOLEFT_INDEXSPLIT ( input, fai, 10 ) -} diff --git a/tests/modules/nf-core/goleft/indexsplit/nextflow.config b/tests/modules/nf-core/goleft/indexsplit/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/goleft/indexsplit/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/goleft/indexsplit/test.yml b/tests/modules/nf-core/goleft/indexsplit/test.yml deleted file mode 100644 index e089286a9323..000000000000 --- a/tests/modules/nf-core/goleft/indexsplit/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: goleft indexsplit test_goleft_indexsplit - command: nextflow run ./tests/modules/nf-core/goleft/indexsplit -entry test_goleft_indexsplit -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/goleft/indexsplit/nextflow.config - tags: - - goleft - - goleft/indexsplit - files: - - path: output/goleft/test.bed - md5sum: 6158ae22773bda2b1380c1f7e324d7a9 - - path: output/goleft/versions.yml diff --git a/tests/modules/nf-core/graphtyper/vcfconcatenate/main.nf b/tests/modules/nf-core/graphtyper/vcfconcatenate/main.nf deleted file mode 100644 index a5fe35ca6a92..000000000000 --- a/tests/modules/nf-core/graphtyper/vcfconcatenate/main.nf +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GRAPHTYPER_VCFCONCATENATE } from '../../../../../modules/nf-core/graphtyper/vcfconcatenate/main.nf' - -workflow test_graphtyper_vcfconcatenate { - - input = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - ] - ] - - GRAPHTYPER_VCFCONCATENATE ( input ) -} diff --git a/tests/modules/nf-core/graphtyper/vcfconcatenate/nextflow.config b/tests/modules/nf-core/graphtyper/vcfconcatenate/nextflow.config deleted file mode 100644 index c7cbbe669b98..000000000000 --- a/tests/modules/nf-core/graphtyper/vcfconcatenate/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GRAPHTYPER_VCFCONCATENATE { - ext.prefix = "prefix" - } -} diff --git a/tests/modules/nf-core/graphtyper/vcfconcatenate/test.yml b/tests/modules/nf-core/graphtyper/vcfconcatenate/test.yml deleted file mode 100644 index 08964bc36800..000000000000 --- a/tests/modules/nf-core/graphtyper/vcfconcatenate/test.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: graphtyper vcfconcatenate test_graphtyper_vcfconcatenate - command: nextflow run ./tests/modules/nf-core/graphtyper/vcfconcatenate -entry test_graphtyper_vcfconcatenate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/graphtyper/vcfconcatenate/nextflow.config - tags: - - graphtyper - - graphtyper/vcfconcatenate - files: - - path: output/graphtyper/prefix.vcf.gz - contains: ["FORMAT data/genomics/sarscov2/bam/test_paired_end.sorted.bam"] - - path: output/graphtyper/prefix.vcf.gz.tbi - - path: output/graphtyper/versions.yml diff --git a/tests/modules/nf-core/gubbins/main.nf b/tests/modules/nf-core/gubbins/main.nf deleted file mode 100644 index f65460d821ea..000000000000 --- a/tests/modules/nf-core/gubbins/main.nf +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GUBBINS } from '../../../../modules/nf-core/gubbins/main.nf' - -workflow test_gubbins { - input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true) - - GUBBINS ( input ) -} diff --git a/tests/modules/nf-core/gubbins/nextflow.config b/tests/modules/nf-core/gubbins/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/gubbins/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/gubbins/test.yml b/tests/modules/nf-core/gubbins/test.yml deleted file mode 100644 index 39b9d738cf26..000000000000 --- a/tests/modules/nf-core/gubbins/test.yml +++ /dev/null @@ -1,23 +0,0 @@ -- name: gubbins - command: nextflow run ./tests/modules/nf-core/gubbins -entry test_gubbins -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gubbins/nextflow.config - tags: - - gubbins - files: - - path: output/gubbins/all_sites.filtered_polymorphic_sites.fasta - md5sum: 4cbfd93868d8ed7d4d8b099eba137134 - - path: output/gubbins/all_sites.recombination_predictions.embl - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/gubbins/all_sites.recombination_predictions.gff - md5sum: f95871e79968340cb82532e2c9b0c92b - - path: output/gubbins/all_sites.branch_base_reconstruction.embl - md5sum: 9e051646d630f528fff58f1f73286006 - - path: output/gubbins/all_sites.summary_of_snp_distribution.vcf - md5sum: 276e62e888ea811577c8ffb2da0b3aff - - path: output/gubbins/all_sites.per_branch_statistics.csv - md5sum: 25e4fdb6681c3709a9add1d5632bbf3e - - path: output/gubbins/all_sites.filtered_polymorphic_sites.phylip - md5sum: 0a77f397a7797c5c3386832745b0c97a - - path: output/gubbins/all_sites.final_tree.tre - md5sum: 6cb251b58307aab11cb4b48792d6cda1 - - path: output/gubbins/all_sites.node_labelled.final_tree.tre - md5sum: e01f965a15924b4f97603b8011c8d3f7 diff --git a/tests/modules/nf-core/hapibd/main.nf b/tests/modules/nf-core/hapibd/main.nf deleted file mode 100644 index 3a7a0deb4da6..000000000000 --- a/tests/modules/nf-core/hapibd/main.nf +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HAPIBD } from '../../../../modules/nf-core/hapibd/main.nf' - -workflow test_hapibd { - - input = [ - [ id:'test', single_end:false ], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) - ] - map = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) - - HAPIBD ( input, map, [] ) -} - -workflow test_hapibd_excludesamples { - - input = [ - [ id:'test', single_end:false ], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) - ] - map = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) - exclude = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/excludeSamples.txt", checkIfExists: true) - - HAPIBD ( input, map, exclude ) -} diff --git a/tests/modules/nf-core/hapibd/nextflow.config b/tests/modules/nf-core/hapibd/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/hapibd/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/hapibd/test.yml b/tests/modules/nf-core/hapibd/test.yml deleted file mode 100644 index 12f5192db221..000000000000 --- a/tests/modules/nf-core/hapibd/test.yml +++ /dev/null @@ -1,21 +0,0 @@ -- name: hapibd test_hapibd - command: nextflow run ./tests/modules/nf-core/hapibd -entry test_hapibd -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hapibd/nextflow.config - tags: - - hapibd - files: - - path: output/hapibd/test.hbd.gz # this is an empty file for this test example - - path: output/hapibd/test.ibd.gz - contains: ["I3019"] - - path: output/hapibd/test.log - contains: ["hap-ibd.jar"] - -- name: hapibd test_hapibd_excludesamples - command: nextflow run ./tests/modules/nf-core/hapibd -entry test_hapibd_excludesamples -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hapibd/nextflow.config - tags: - - hapibd - files: - - path: output/hapibd/test.hbd.gz # this is an empty file for this test example - - path: output/hapibd/test.ibd.gz - contains: ["I3019"] - - path: output/hapibd/test.log - contains: ["hap-ibd.jar"] diff --git a/tests/modules/nf-core/haplogrep2/classify/main.nf b/tests/modules/nf-core/haplogrep2/classify/main.nf deleted file mode 100644 index 6385aed5de7f..000000000000 --- a/tests/modules/nf-core/haplogrep2/classify/main.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HAPLOGREP2_CLASSIFY } from '../../../../../modules/nf-core/haplogrep2/classify/main.nf' - -workflow test_haplogrep2_classify { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_mito_vcf'], checkIfExists: true) - ] - format = 'vcf' - - HAPLOGREP2_CLASSIFY ( input,format ) -} diff --git a/tests/modules/nf-core/haplogrep2/classify/nextflow.config b/tests/modules/nf-core/haplogrep2/classify/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/haplogrep2/classify/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/haplogrep2/classify/test.yml b/tests/modules/nf-core/haplogrep2/classify/test.yml deleted file mode 100644 index a182a080e01d..000000000000 --- a/tests/modules/nf-core/haplogrep2/classify/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: haplogrep2 classify - command: nextflow run ./tests/modules/nf-core/haplogrep2/classify -entry test_haplogrep2_classify -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/haplogrep2/classify/nextflow.config - tags: - - haplogrep2 - - haplogrep2/classify - files: - - path: output/haplogrep2/test.txt - - path: output/haplogrep2/versions.yml - -- name: haplogrep2 classify stubs - command: nextflow run ./tests/modules/nf-core/haplogrep2/classify -stub-run -entry test_haplogrep2_classify -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/haplogrep2/classify/nextflow.config - tags: - - haplogrep2 - - haplogrep2/classify - files: - - path: output/haplogrep2/test.txt - - path: output/haplogrep2/versions.yml diff --git a/tests/modules/nf-core/hmmer/hmmbuild/main.nf b/tests/modules/nf-core/hmmer/hmmbuild/main.nf deleted file mode 100644 index 7bd3a4b3a5f9..000000000000 --- a/tests/modules/nf-core/hmmer/hmmbuild/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HMMER_HMMBUILD } from '../../../../../modules/nf-core/hmmer/hmmbuild/main.nf' - -workflow test_hmmer_hmmbuild { - - input = [ - [ id: 'PF14720' ], // meta map - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) - ] - - HMMER_HMMBUILD ( input, [] ) -} diff --git a/tests/modules/nf-core/hmmer/hmmbuild/nextflow.config b/tests/modules/nf-core/hmmer/hmmbuild/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/hmmer/hmmbuild/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/hmmer/hmmbuild/test.yml b/tests/modules/nf-core/hmmer/hmmbuild/test.yml deleted file mode 100644 index be321bf489a1..000000000000 --- a/tests/modules/nf-core/hmmer/hmmbuild/test.yml +++ /dev/null @@ -1,12 +0,0 @@ -- name: hmmer hmmbuild test_hmmer_hmmbuild - command: nextflow run ./tests/modules/nf-core/hmmer/hmmbuild -entry test_hmmer_hmmbuild -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hmmer/hmmbuild/nextflow.config - tags: - - hmmer - - hmmer/hmmbuild - files: - - path: output/hmmer/PF14720.hmm.gz - contains: - - "LENG 80" - - path: output/hmmer/versions.yml - contains: - - "hmmer:" diff --git a/tests/modules/nf-core/hmmer/hmmfetch/main.nf b/tests/modules/nf-core/hmmer/hmmfetch/main.nf deleted file mode 100644 index db24e553a4ec..000000000000 --- a/tests/modules/nf-core/hmmer/hmmfetch/main.nf +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HMMER_HMMFETCH } from '../../../../../modules/nf-core/hmmer/hmmfetch/main.nf' - -workflow test_hmmer_hmmfetch_key { - - input = [ - [ id:'test', single_end:false ], - file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') - ] - - HMMER_HMMFETCH ( input, '16S_rRNA', [], [] ) -} - -workflow test_hmmer_hmmfetch_keyfile { - - input = [ - [ id:'test', single_end:false ], - file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') - ] - - Channel - .of('16S_rRNA', '23S_rRNA') - .collectFile(name: 'keys.txt', newLine: true) - .set { keyfile } - - HMMER_HMMFETCH ( input, [], keyfile, [] ) -} - -workflow test_hmmer_hmmfetch_index { - - input = [ - [ id:'test', single_end:false ], - file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') - ] - - HMMER_HMMFETCH ( input, [], [], [] ) -} diff --git a/tests/modules/nf-core/hmmer/hmmfetch/nextflow.config b/tests/modules/nf-core/hmmer/hmmfetch/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/hmmer/hmmfetch/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/hmmer/hmmfetch/test.yml b/tests/modules/nf-core/hmmer/hmmfetch/test.yml deleted file mode 100644 index f602892a5864..000000000000 --- a/tests/modules/nf-core/hmmer/hmmfetch/test.yml +++ /dev/null @@ -1,29 +0,0 @@ -- name: hmmer hmmfetch test_hmmer_hmmfetch_key - command: nextflow run ./tests/modules/nf-core/hmmer/hmmfetch -entry test_hmmer_hmmfetch_key -c ./tests/config/nextflow.config - tags: - - hmmer/hmmfetch - - hmmer - files: - - path: output/hmmer/test.hmm - md5sum: 0328406a7469af6f24e2157b0367705f - - path: output/hmmer/versions.yml - -- name: hmmer hmmfetch test_hmmer_hmmfetch_keyfile - command: nextflow run ./tests/modules/nf-core/hmmer/hmmfetch -entry test_hmmer_hmmfetch_keyfile -c ./tests/config/nextflow.config - tags: - - hmmer/hmmfetch - - hmmer - files: - - path: output/hmmer/test.hmm - md5sum: 0e5c7e77342ec91bc6fac2a7a0228d08 - - path: output/hmmer/versions.yml - -- name: hmmer hmmfetch test_hmmer_hmmfetch_index - command: nextflow run ./tests/modules/nf-core/hmmer/hmmfetch -entry test_hmmer_hmmfetch_index -c ./tests/config/nextflow.config - tags: - - hmmer/hmmfetch - - hmmer - files: - - path: output/hmmer/arc.hmm.ssi - md5sum: 17a7bb35662baabb5b1474660d072fb6 - - path: output/hmmer/versions.yml diff --git a/tests/modules/nf-core/homer/annotatepeaks/main.nf b/tests/modules/nf-core/homer/annotatepeaks/main.nf deleted file mode 100644 index cfd52c1ba494..000000000000 --- a/tests/modules/nf-core/homer/annotatepeaks/main.nf +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HOMER_ANNOTATEPEAKS } from '../../../../../modules/nf-core/homer/annotatepeaks/main.nf' - -workflow test_homer_annotatepeaks { - input = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - HOMER_ANNOTATEPEAKS ( input, fasta, gtf ) -} diff --git a/tests/modules/nf-core/homer/annotatepeaks/nextflow.config b/tests/modules/nf-core/homer/annotatepeaks/nextflow.config deleted file mode 100644 index 86470e916848..000000000000 --- a/tests/modules/nf-core/homer/annotatepeaks/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.args = {"-annStats ${meta.id}.annStats.txt"} - -} diff --git a/tests/modules/nf-core/homer/annotatepeaks/test.yml b/tests/modules/nf-core/homer/annotatepeaks/test.yml deleted file mode 100644 index 9a07bc5d597e..000000000000 --- a/tests/modules/nf-core/homer/annotatepeaks/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: homer annotatepeaks test_homer_annotatepeaks - command: nextflow run ./tests/modules/nf-core/homer/annotatepeaks -entry test_homer_annotatepeaks -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/homer/annotatepeaks/nextflow.config - tags: - - homer - - homer/annotatepeaks - files: - - path: output/homer/test.annotatePeaks.txt - - path: output/homer/test.annStats.txt diff --git a/tests/modules/nf-core/hypo/main.nf b/tests/modules/nf-core/hypo/main.nf deleted file mode 100644 index 89b169fc58eb..000000000000 --- a/tests/modules/nf-core/hypo/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HYPO } from '../../../../modules/nf-core/hypo/main.nf' - -workflow test_hypo { - - bam_sr = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - reads = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) - ] - ] - draft = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - genome_size = 29903 - reads_coverage = 5 - HYPO ( bam_sr, reads, draft, genome_size, reads_coverage ) -} diff --git a/tests/modules/nf-core/hypo/nextflow.config b/tests/modules/nf-core/hypo/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/hypo/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/hypo/test.yml b/tests/modules/nf-core/hypo/test.yml deleted file mode 100644 index f298d04ea897..000000000000 --- a/tests/modules/nf-core/hypo/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: "hypo" - command: nextflow run ./tests/modules/nf-core/hypo -entry test_hypo -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hypo/nextflow.config - tags: - - "hypo" - files: - - path: "output/hypo/test.fasta" - md5sum: d326ff4fc91e25617c43d678f68187ad - - path: "output/hypo/versions.yml" - md5sum: 34233e4c5530683bf3c9e890e2b20e91 diff --git a/tests/modules/nf-core/idr/main.nf b/tests/modules/nf-core/idr/main.nf deleted file mode 100644 index f532e8f59943..000000000000 --- a/tests/modules/nf-core/idr/main.nf +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { IDR } from '../../../../modules/nf-core/idr/main.nf' - -workflow test_idr_narrowpeak { - - input = [ - file(params.test_data['homo_sapiens']['illumina']['test_narrowpeak'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_narrowpeak'], checkIfExists: true) - ] - - IDR ( input, 'narrowPeak', 'test' ) -} - -workflow test_idr_broadpeak { - - input = [ - file(params.test_data['homo_sapiens']['illumina']['test_broadpeak'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_broadpeak'], checkIfExists: true) - ] - - IDR ( input, 'broadPeak', 'test' ) -} - -workflow test_idr_noprefix { - - input = [ - file(params.test_data['homo_sapiens']['illumina']['test_narrowpeak'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_narrowpeak'], checkIfExists: true) - ] - - IDR ( input, 'narrowPeak', '' ) -} diff --git a/tests/modules/nf-core/idr/nextflow.config b/tests/modules/nf-core/idr/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/idr/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/idr/test.yml b/tests/modules/nf-core/idr/test.yml deleted file mode 100644 index 42a4b1bda5ae..000000000000 --- a/tests/modules/nf-core/idr/test.yml +++ /dev/null @@ -1,35 +0,0 @@ -- name: idr test_idr_narrowpeak - command: nextflow run ./tests/modules/nf-core/idr -entry test_idr_narrowpeak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/idr/nextflow.config - tags: - - idr - files: - - path: output/idr/test.idrValues.txt - md5sum: 09be837cc6abbc3eb5958b74802eea55 - - path: output/idr/test.idrValues.txt.png - md5sum: 4a7143ccc0ccadb37c2317bf626e6d96 - - path: output/idr/test.log.txt - md5sum: 6443507ac66b9d3b64bc56b78328083e - -- name: idr test_idr_broadpeak - command: nextflow run ./tests/modules/nf-core/idr -entry test_idr_broadpeak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/idr/nextflow.config - tags: - - idr - files: - - path: output/idr/test.idrValues.txt - md5sum: 387441c716815e4caec3e70a2cc11a4a - - path: output/idr/test.idrValues.txt.png - md5sum: 7204083ca5b920b4215a5991c12cb4e7 - - path: output/idr/test.log.txt - md5sum: e6917133112b5cec135c182ffac19237 - -- name: idr test_idr_noprefix - command: nextflow run ./tests/modules/nf-core/idr -entry test_idr_noprefix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/idr/nextflow.config - tags: - - idr - files: - - path: output/idr/idrValues.txt - md5sum: 09be837cc6abbc3eb5958b74802eea55 - - path: output/idr/idrValues.txt.png - md5sum: 4a7143ccc0ccadb37c2317bf626e6d96 - - path: output/idr/log.txt - md5sum: 6443507ac66b9d3b64bc56b78328083e diff --git a/tests/modules/nf-core/ivar/consensus/main.nf b/tests/modules/nf-core/ivar/consensus/main.nf deleted file mode 100644 index 37ce0f8f17ec..000000000000 --- a/tests/modules/nf-core/ivar/consensus/main.nf +++ /dev/null @@ -1,29 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { IVAR_CONSENSUS } from '../../../../../modules/nf-core/ivar/consensus/main.nf' - -workflow test_ivar_consensus { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - save_mpileup = false - - IVAR_CONSENSUS ( input, fasta, save_mpileup) -} - -workflow test_ivar_consensus_mpileup { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - save_mpileup = true - - IVAR_CONSENSUS ( input, fasta, save_mpileup) -} diff --git a/tests/modules/nf-core/ivar/consensus/nextflow.config b/tests/modules/nf-core/ivar/consensus/nextflow.config deleted file mode 100644 index 7407619ad579..000000000000 --- a/tests/modules/nf-core/ivar/consensus/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: IVAR_CONSENSUS { - ext.args2 = '-aa -A -d 0 -Q 0' - } - -} diff --git a/tests/modules/nf-core/ivar/consensus/test.yml b/tests/modules/nf-core/ivar/consensus/test.yml deleted file mode 100644 index b676caf11e19..000000000000 --- a/tests/modules/nf-core/ivar/consensus/test.yml +++ /dev/null @@ -1,22 +0,0 @@ -- name: ivar consensus test_ivar_consensus - command: nextflow run ./tests/modules/nf-core/ivar/consensus -entry test_ivar_consensus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/consensus/nextflow.config - tags: - - ivar - - ivar/consensus - files: - - path: output/ivar/test.fa - md5sum: 9e21a64818f4302b4dece5480fa5e8b8 - - path: output/ivar/test.qual.txt - md5sum: 68b329da9893e34099c7d8ad5cb9c940 - -- name: ivar consensus test_ivar_consensus_mpileup - command: nextflow run ./tests/modules/nf-core/ivar/consensus -entry test_ivar_consensus_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/consensus/nextflow.config - tags: - - ivar - - ivar/consensus - files: - - path: output/ivar/test.fa - md5sum: 9e21a64818f4302b4dece5480fa5e8b8 - - path: output/ivar/test.qual.txt - md5sum: 68b329da9893e34099c7d8ad5cb9c940 - - path: output/ivar/test.mpileup diff --git a/tests/modules/nf-core/ivar/variants/main.nf b/tests/modules/nf-core/ivar/variants/main.nf deleted file mode 100644 index b8dd56b5ba38..000000000000 --- a/tests/modules/nf-core/ivar/variants/main.nf +++ /dev/null @@ -1,47 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { IVAR_VARIANTS } from '../../../../../modules/nf-core/ivar/variants/main.nf' - -workflow test_ivar_variants_no_gff_no_mpileup { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - gff = [] - save_mpileup = false - - IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup ) -} - -workflow test_ivar_variants_no_gff_with_mpileup { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - gff = [] - save_mpileup = true - - IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup ) -} - -workflow test_ivar_variants_with_gff_with_mpileup { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) - save_mpileup = true - - IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup ) -} diff --git a/tests/modules/nf-core/ivar/variants/nextflow.config b/tests/modules/nf-core/ivar/variants/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/ivar/variants/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/ivar/variants/test.yml b/tests/modules/nf-core/ivar/variants/test.yml deleted file mode 100644 index 9fc3506f6e92..000000000000 --- a/tests/modules/nf-core/ivar/variants/test.yml +++ /dev/null @@ -1,30 +0,0 @@ -- name: ivar variants no gff no mpileup - command: nextflow run ./tests/modules/nf-core/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/variants/nextflow.config - tags: - - ivar - - ivar/variants - files: - - path: output/ivar/test.tsv - md5sum: 76c93420121bb891fa275f716142a157 - -- name: ivar variants no gff with mpileup - command: nextflow run ./tests/modules/nf-core/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c ./tests/config/nextflow.config --save_mpileup -c ./tests/modules/nf-core/ivar/variants/nextflow.config - tags: - - ivar - - ivar/variants - files: - - path: output/ivar/test.tsv - md5sum: 76c93420121bb891fa275f716142a157 - - path: output/ivar/test.mpileup - md5sum: 958e6bead4103d72026f80153b6b5150 - -- name: ivar variants with gff with mpileup - command: nextflow run ./tests/modules/nf-core/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c ./tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup -c ./tests/modules/nf-core/ivar/variants/nextflow.config - tags: - - ivar - - ivar/variants - files: - - path: output/ivar/test.tsv - md5sum: 2cf6c48b55e0e81155ff310d48de94df - - path: output/ivar/test.mpileup - md5sum: 958e6bead4103d72026f80153b6b5150 diff --git a/tests/modules/nf-core/legsta/main.nf b/tests/modules/nf-core/legsta/main.nf deleted file mode 100644 index b74a9cf278a6..000000000000 --- a/tests/modules/nf-core/legsta/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { LEGSTA } from '../../../../modules/nf-core/legsta/main.nf' - -workflow test_legsta { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - LEGSTA ( input ) -} diff --git a/tests/modules/nf-core/legsta/nextflow.config b/tests/modules/nf-core/legsta/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/legsta/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/legsta/test.yml b/tests/modules/nf-core/legsta/test.yml deleted file mode 100644 index 6d193422d341..000000000000 --- a/tests/modules/nf-core/legsta/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: legsta test_legsta - command: nextflow run ./tests/modules/nf-core/legsta -entry test_legsta -c ./tests/config/nextflow.config - tags: - - legsta - files: - - path: output/legsta/test.tsv - md5sum: c493bdd19335de4828aa8b4e3ce7e1f8 - - path: output/legsta/versions.yml - md5sum: d16c5f6fd68d2bcc2c71954e3342aabe diff --git a/tests/modules/nf-core/mapdamage2/main.nf b/tests/modules/nf-core/mapdamage2/main.nf deleted file mode 100644 index 47e550c6e964..000000000000 --- a/tests/modules/nf-core/mapdamage2/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { MAPDAMAGE2 } from '../../../../modules/nf-core/mapdamage2/main.nf' - -workflow test_mapdamage2 { - - input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - - MAPDAMAGE2 ( input, fasta ) -} diff --git a/tests/modules/nf-core/mapdamage2/nextflow.config b/tests/modules/nf-core/mapdamage2/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/mapdamage2/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/mapdamage2/test.yml b/tests/modules/nf-core/mapdamage2/test.yml deleted file mode 100644 index 4ac70c72356b..000000000000 --- a/tests/modules/nf-core/mapdamage2/test.yml +++ /dev/null @@ -1,25 +0,0 @@ -- name: mapdamage2 test_mapdamage2 - command: nextflow run ./tests/modules/nf-core/mapdamage2 -entry test_mapdamage2 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mapdamage2/nextflow.config - tags: - - mapdamage2 - files: - - path: output/mapdamage2/results_test.paired_end.sorted/3pGtoA_freq.txt - md5sum: 3b300b8d2842441675cb2b56740801f0 - - path: output/mapdamage2/results_test.paired_end.sorted/5pCtoT_freq.txt - md5sum: 4c27465cd02e1fb8bf6fb2b01e98446d - - path: output/mapdamage2/results_test.paired_end.sorted/Fragmisincorporation_plot.pdf - - path: output/mapdamage2/results_test.paired_end.sorted/Runtime_log.txt - - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_correct_prob.csv - - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_hist.pdf - - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_iter.csv - - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_iter_summ_stat.csv - - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_post_pred.pdf - - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_trace.pdf - - path: output/mapdamage2/results_test.paired_end.sorted/dnacomp.txt - md5sum: 4244d9fa554bbfeebbcea8eba3ad6466 - - path: output/mapdamage2/results_test.paired_end.sorted/dnacomp_genome.csv - md5sum: ea91a3d205717d3c6b3e0b77bb840945 - - path: output/mapdamage2/results_test.paired_end.sorted/lgdistribution.txt - md5sum: f86dfc04b1fff4337cc91add6356e3a0 - - path: output/mapdamage2/results_test.paired_end.sorted/misincorporation.txt - md5sum: 1c89b4c96d1f8996c3d0879cad5129a5 diff --git a/tests/modules/nf-core/mmseqs/databases/main.nf b/tests/modules/nf-core/mmseqs/databases/main.nf deleted file mode 100644 index bd0bb9d4eb60..000000000000 --- a/tests/modules/nf-core/mmseqs/databases/main.nf +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { MMSEQS_DATABASES } from '../../../../../modules/nf-core/mmseqs/databases/main.nf' - -workflow test_mmseqs_databases { - - input = "SILVA" - - MMSEQS_DATABASES ( input ) -} diff --git a/tests/modules/nf-core/mmseqs/databases/nextflow.config b/tests/modules/nf-core/mmseqs/databases/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/mmseqs/databases/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/mmseqs/databases/test.yml b/tests/modules/nf-core/mmseqs/databases/test.yml deleted file mode 100644 index dee34721b304..000000000000 --- a/tests/modules/nf-core/mmseqs/databases/test.yml +++ /dev/null @@ -1,18 +0,0 @@ -- name: mmseqs databases test_mmseqs_databases - command: nextflow run ./tests/modules/nf-core/mmseqs/databases -entry test_mmseqs_databases -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mmseqs/databases/nextflow.config - tags: - - mmseqs - - mmseqs/databases - files: - - path: output/mmseqs/mmseqs_database/database - - path: output/mmseqs/mmseqs_database/database.dbtype - - path: output/mmseqs/mmseqs_database/database.index - - path: output/mmseqs/mmseqs_database/database.lookup - - path: output/mmseqs/mmseqs_database/database.source - - path: output/mmseqs/mmseqs_database/database.version - - path: output/mmseqs/mmseqs_database/database_h - - path: output/mmseqs/mmseqs_database/database_h.dbtype - - path: output/mmseqs/mmseqs_database/database_h.index - - path: output/mmseqs/mmseqs_database/database_mapping - - path: output/mmseqs/mmseqs_database/database_taxonomy - - path: output/mmseqs/versions.yml diff --git a/tests/modules/nf-core/purecn/intervalfile/main.nf b/tests/modules/nf-core/purecn/intervalfile/main.nf deleted file mode 100644 index 5c36c613a9df..000000000000 --- a/tests/modules/nf-core/purecn/intervalfile/main.nf +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PURECN_INTERVALFILE } from '../../../../../modules/nf-core/purecn/intervalfile/main.nf' - -workflow test_purecn_intervalfile { - - meta = [id: "test"] - bed_input = [meta, file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)] - sequence = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - meta2 = [id: "fasta"] - sequence_input = [meta2, sequence] - genome = Channel.value("hg38") - - PURECN_INTERVALFILE ( bed_input, sequence_input, genome ) -} diff --git a/tests/modules/nf-core/purecn/intervalfile/nextflow.config b/tests/modules/nf-core/purecn/intervalfile/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/purecn/intervalfile/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/purecn/intervalfile/test.yml b/tests/modules/nf-core/purecn/intervalfile/test.yml deleted file mode 100644 index 7bc0595a223f..000000000000 --- a/tests/modules/nf-core/purecn/intervalfile/test.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: "purecn intervalfile" - command: nextflow run ./tests/modules/nf-core/purecn/intervalfile -entry test_purecn_intervalfile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/purecn/intervalfile/nextflow.config - tags: - - "purecn" - - "purecn/intervalfile" - files: - - path: "output/purecn/test.txt" - md5sum: 198d037d5f423d995f3da98d6cf92867 - - path: "output/purecn/versions.yml" - md5sum: 01226f36faf8d39f23d655b6837eba08