diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 760d9136e47..89a74294bcf 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -646,6 +646,8 @@ jobs: - name: Install nf-test uses: nf-core/setup-nf-test@v1 + with: + version: ${{ env.NFTEST_VER }} - name: Setup apptainer if: matrix.profile == 'singularity' diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 16c937f2a0b..ae3d4a2c778 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: - id: renovate-config-validator # use ruff for python files - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.1 + rev: v0.6.2 hooks: - id: ruff files: \.py$ diff --git a/modules/nf-core/bandage/image/tests/main.nf.test b/modules/nf-core/bandage/image/tests/main.nf.test new file mode 100644 index 00000000000..160281f9b83 --- /dev/null +++ b/modules/nf-core/bandage/image/tests/main.nf.test @@ -0,0 +1,40 @@ + +nextflow_process { + + name "Test Process BANDAGE_IMAGE" + script "../main.nf" + process "BANDAGE_IMAGE" + + tag "modules" + tag "modules_nfcore" + tag "bandage" + tag "bandage/image" + + test("test-bandage-image") { + + when { + process { + """ + input[0] = [ + [ id:'B-3106' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.png[0][1]).name, + file(process.out.svg[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/bandage/image/tests/main.nf.test.snap b/modules/nf-core/bandage/image/tests/main.nf.test.snap new file mode 100644 index 00000000000..1f260eca921 --- /dev/null +++ b/modules/nf-core/bandage/image/tests/main.nf.test.snap @@ -0,0 +1,22 @@ +{ + "test-bandage-image": { + "content": [ + "B-3106.png", + [ + " xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" version=\"1.2\" baseProfile=\"tiny\">", + "Qt SVG Document", + "Generated with Qt", + "", + "" + ], + [ + "versions.yml:md5,443fd5f11eb36f013a1863e66d0eea21" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T15:18:46.613049" + } +} \ No newline at end of file diff --git a/modules/nf-core/bbmap/bbnorm/meta.yml b/modules/nf-core/bbmap/bbnorm/meta.yml index 6c8426f88f1..052c5b534d6 100644 --- a/modules/nf-core/bbmap/bbnorm/meta.yml +++ b/modules/nf-core/bbmap/bbnorm/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" tool_dev_url: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/" - licence: "BBMap - Bushnell B. - sourceforge.net/projects/bbmap/" + licence: ["BBMap - Bushnell B. - sourceforge.net/projects/bbmap/"] input: - meta: type: map diff --git a/modules/nf-core/bbmap/bbnorm/tests/main.nf.test b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test new file mode 100644 index 00000000000..fc17dc1c8fa --- /dev/null +++ b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test @@ -0,0 +1,128 @@ + +nextflow_process { + + name "Test Process BBMAP_BBNORM" + script "../main.nf" + process "BBMAP_BBNORM" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "bbmap" + tag "bbmap/bbnorm" + + test("test-bbmap-bbnorm-se") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.fastq[0][1]).linesGzip, + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-bbmap-bbnorm-pe") { + + when { + process { + """ + input[0] = [ + [ 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) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fastq[0][1].collect { path(it).linesGzip[0..1] }, + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-bbmap-bbnorm-interleaved") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.fastq[0][1]).linesGzip[3..7], + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-bbmap-bbnorm-multiple-input") { + + when { + process { + """ + input[0] = [ + [id:'test', single_end:true ], + [ + 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) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.fastq[0][1]).linesGzip[3..7], + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap new file mode 100644 index 00000000000..1d7b2438abd --- /dev/null +++ b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap @@ -0,0 +1,81 @@ +{ + "test-bbmap-bbnorm-interleaved": { + "content": [ + [ + "A/AA//EEAEA/E/AEEEE6EE/EEEA/6AEEEEEEEEE6EEEAEAEE//A/EEEEEE//E/E/A//E/E/< + all_files << file + } + + def all_file_names = all_files.collect { it.name }.toSorted() + + def stable_file_names = [ + 'chr1_index_k13_c15_b1.block' + ] + + def stable_files = all_files.findAll { it.name in stable_file_names }.toSorted() + + assert snapshot( + all_file_names, + stable_files, + process.out.versions[0] + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/bbmap/index/tests/main.nf.test.snap b/modules/nf-core/bbmap/index/tests/main.nf.test.snap new file mode 100644 index 00000000000..9e691dd41ec --- /dev/null +++ b/modules/nf-core/bbmap/index/tests/main.nf.test.snap @@ -0,0 +1,23 @@ +{ + "test-bbmap-index": { + "content": [ + [ + "chr1.chrom.gz", + "chr1_index_k13_c15_b1.block", + "chr1_index_k13_c15_b1.block2.gz", + "info.txt", + "scaffolds.txt.gz", + "summary.txt" + ], + [ + "chr1_index_k13_c15_b1.block:md5,9f0d9a7413c1d2c16cc24555b2381163" + ], + "versions.yml:md5,00db75f2ebfcae6002a29c49a476dda1" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:41:14.388643" + } +} \ No newline at end of file diff --git a/modules/nf-core/bbmap/pileup/tests/main.nf.test b/modules/nf-core/bbmap/pileup/tests/main.nf.test new file mode 100644 index 00000000000..583f407f770 --- /dev/null +++ b/modules/nf-core/bbmap/pileup/tests/main.nf.test @@ -0,0 +1,35 @@ + +nextflow_process { + + name "Test Process BBMAP_PILEUP" + script "../main.nf" + process "BBMAP_PILEUP" + + tag "modules" + tag "modules_nfcore" + tag "bbmap" + tag "bbmap/pileup" + + test("test-bbmap-pileup") { + + 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) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap b/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap new file mode 100644 index 00000000000..f5e7e720d02 --- /dev/null +++ b/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap @@ -0,0 +1,55 @@ +{ + "test-bbmap-pileup": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.coverage.stats.txt:md5,c3fc9d0681589b69e3301ca3cb27b7a4" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.coverage.hist.txt:md5,96915920ef42ddc9483457dd4585a088" + ] + ], + "2": [ + "versions.yml:md5,e293e3ed6387ce89f3443050f36fb079" + ], + "covstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.coverage.stats.txt:md5,c3fc9d0681589b69e3301ca3cb27b7a4" + ] + ], + "hist": [ + [ + { + "id": "test", + "single_end": false + }, + "test.coverage.hist.txt:md5,96915920ef42ddc9483457dd4585a088" + ] + ], + "versions": [ + "versions.yml:md5,e293e3ed6387ce89f3443050f36fb079" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:33:48.464105" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index f73111bb789..c3b8b19652c 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -8,9 +8,7 @@ process BCFTOOLS_ANNOTATE { 'biocontainers/bcftools:1.20--h8b25389_0' }" input: - tuple val(meta), path(input), path(index) - path(annotations) - path(annotations_index) + tuple val(meta), path(input), path(index), path(annotations), path(annotations_index) path(header_lines) output: diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test index fa499de763d..3a5c493314f 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -9,20 +9,21 @@ nextflow_process { tag "bcftools" tag "bcftools/annotate" - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_output") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output") { config "./vcf.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map + 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/test.vcf.gz.tbi', checkIfExists: true)] - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = [] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + 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] = [] """ } } @@ -39,20 +40,21 @@ nextflow_process { } - test("sarscov2 - [vcf, []] annotation, annotation_tbi, [] - vcf_output") { + test("sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output") { config "./vcf.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), - []] - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = [] + [], + 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] = [] """ } } @@ -68,20 +70,21 @@ nextflow_process { } } - test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index") { config "./vcf_gz_index.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map + 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/test.vcf.gz.tbi', checkIfExists: true)] - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = [] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + 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] = [] """ } } @@ -101,20 +104,21 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_csi") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi") { config "./vcf_gz_index_csi.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map + 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/test.vcf.gz.tbi', checkIfExists: true)] - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = [] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + 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] = [] """ } } @@ -134,20 +138,21 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_tbi") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi") { config "./vcf_gz_index_tbi.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map + 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/test.vcf.gz.tbi', checkIfExists: true)] - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = [] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + 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] = [] """ } } @@ -166,20 +171,21 @@ nextflow_process { } } - test("sarscov2 - [vcf, []], annotation, annotation_tbi, header - bcf_output") { + test("sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output") { config "./bcf.config" when { process { """ - input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), - []]) - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = Channel.of( + [], + 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] = Channel.of( '##INFO=', '##INFO=' ).collectFile(name:"headers.vcf", newLine:true) @@ -199,7 +205,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub") { config "./vcf.config" options "-stub" @@ -207,13 +213,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map + 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/test.vcf.gz.tbi', checkIfExists: true)] - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = [] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + 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] = [] """ } } @@ -227,7 +234,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub") { config "./vcf_gz_index.config" options "-stub" @@ -235,13 +242,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map + 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/test.vcf.gz.tbi', checkIfExists: true)] - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = [] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + 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] = [] """ } } @@ -256,7 +264,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_csi - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub") { config "./vcf_gz_index_csi.config" options "-stub" @@ -264,13 +272,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map + 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/test.vcf.gz.tbi', checkIfExists: true)] - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = [] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + 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] = [] """ } } @@ -285,7 +294,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_tbi - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub") { config "./vcf_gz_index_tbi.config" options "-stub" @@ -293,13 +302,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map + 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/test.vcf.gz.tbi', checkIfExists: true)] - - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - input[3] = [] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + 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] = [] """ } } diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap index 8fd8d11dccf..bac2224a3b5 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -1,38 +1,5 @@ { - "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_tbi": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi" - ] - ], - [ - - ], - [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-12T16:39:23.802873" - }, - "sarscov2 - [vcf, []] annotation, annotation_tbi, [] - vcf_output": { + "bcf": { "content": [ [ [ @@ -40,7 +7,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.bcf" ] ], [ @@ -51,9 +18,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:38:57.039285" + "timestamp": "2024-06-12T16:39:33.331888" }, - "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_csi": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index": { "content": [ [ [ @@ -84,9 +51,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:15.152697" + "timestamp": "2024-08-15T10:07:59.658031137" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub": { "content": [ { "0": [ @@ -102,13 +69,25 @@ ], "2": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "3": [ "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" ], "csi": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "tbi": [ @@ -131,9 +110,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:41.994785" + "timestamp": "2024-08-15T10:09:05.096883418" }, - "bcf": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi": { "content": [ [ [ @@ -141,7 +120,19 @@ "id": "test", "single_end": false }, - "test_ann.bcf" + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" ] ], [ @@ -152,9 +143,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:33.331888" + "timestamp": "2024-08-15T10:08:10.581301219" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_tbi - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub": { "content": [ { "0": [ @@ -167,13 +158,7 @@ ] ], "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "2": [ @@ -185,13 +170,7 @@ ], "tbi": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "vcf": [ [ @@ -211,9 +190,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:40:13.835994" + "timestamp": "2024-08-15T10:08:43.975017625" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_output": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi": { "content": [ [ [ @@ -223,6 +202,18 @@ }, "test_vcf.vcf.gz" ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + ], [ "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" @@ -232,9 +223,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:38:48.368629" + "timestamp": "2024-08-15T10:08:21.354059092" }, - "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output": { "content": [ [ [ @@ -246,15 +237,24 @@ ] ], [ - - ], + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:07:37.788393317" + }, + "sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output": { + "content": [ [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi" + "test_vcf.vcf.gz" ] ], [ @@ -265,9 +265,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:05.608108" + "timestamp": "2024-08-15T10:07:48.500746325" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub": { "content": [ { "0": [ @@ -280,31 +280,31 @@ ] ], "1": [ - - ], - "2": [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "2": [ + ], "3": [ "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" ], "csi": [ + + ], + "tbi": [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "tbi": [ - ], "vcf": [ [ @@ -324,9 +324,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:54.842082" + "timestamp": "2024-08-15T10:09:16.094918834" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_csi - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub": { "content": [ { "0": [ @@ -383,6 +383,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:40:04.074052" + "timestamp": "2024-08-15T10:08:54.366358502" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/roh/tests/main.nf.test b/modules/nf-core/bcftools/roh/tests/main.nf.test new file mode 100644 index 00000000000..bb73b80c024 --- /dev/null +++ b/modules/nf-core/bcftools/roh/tests/main.nf.test @@ -0,0 +1,67 @@ + +nextflow_process { + + name "Test Process BCFTOOLS_ROH" + script "../main.nf" + process "BCFTOOLS_ROH" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/roh" + + test("test-bcftools-roh") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // 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/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [[],[]] + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-bcftools-roh-stub") { + options '-stub' + when { + process { + """ + input[0] = [ [ id:'test' ], // 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/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [[],[]] + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bcftools/roh/tests/main.nf.test.snap b/modules/nf-core/bcftools/roh/tests/main.nf.test.snap new file mode 100644 index 00000000000..3b008a01e98 --- /dev/null +++ b/modules/nf-core/bcftools/roh/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "test-bcftools-roh": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.roh:md5,853de778be3030754be40e11be0aa557" + ] + ], + "1": [ + "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710" + ], + "roh": [ + [ + { + "id": "test" + }, + "test.roh:md5,853de778be3030754be40e11be0aa557" + ] + ], + "versions": [ + "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:19:06.961553" + }, + "test-bcftools-roh-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.roh:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710" + ], + "roh": [ + [ + { + "id": "test" + }, + "test.roh:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:19:11.161719" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/split/tests/main.nf.test b/modules/nf-core/bcftools/split/tests/main.nf.test new file mode 100644 index 00000000000..00328b2004c --- /dev/null +++ b/modules/nf-core/bcftools/split/tests/main.nf.test @@ -0,0 +1,40 @@ + +nextflow_process { + + name "Test Process BCFTOOLS_SPLIT" + script "../main.nf" + process "BCFTOOLS_SPLIT" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/split" + + test("test-bcftools-split") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // 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/test.genome.vcf.gz.tbi', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.split_vcf[0][1]).vcf.variantsMD5, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/bcftools/split/tests/main.nf.test.snap b/modules/nf-core/bcftools/split/tests/main.nf.test.snap new file mode 100644 index 00000000000..c1a3c98578c --- /dev/null +++ b/modules/nf-core/bcftools/split/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-bcftools-split": { + "content": [ + "ecf3973f634b7baa1c13e60bfb77a174", + [ + "versions.yml:md5,a1c58d82f1e5c0fed394bfb865f57fd9" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:16:45.077115" + } +} \ No newline at end of file diff --git a/modules/nf-core/beagle5/beagle/meta.yml b/modules/nf-core/beagle5/beagle/meta.yml index 03b50869270..51b9c6b6997 100644 --- a/modules/nf-core/beagle5/beagle/meta.yml +++ b/modules/nf-core/beagle5/beagle/meta.yml @@ -3,13 +3,14 @@ description: Beagle v5.2 is a software package for phasing genotypes and for imp keywords: - phasing - imputation + - genotype tools: - "beagle5": description: "Beagle is a software package for phasing genotypes and for imputing ungenotyped markers." homepage: "https://faculty.washington.edu/browning/beagle/b5_2.html" documentation: "https://faculty.washington.edu/browning/beagle/beagle_5.2_13Oct21.pdf" doi: "10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/beagle5/beagle/tests/main.nf.test b/modules/nf-core/beagle5/beagle/tests/main.nf.test new file mode 100644 index 00000000000..2763708e273 --- /dev/null +++ b/modules/nf-core/beagle5/beagle/tests/main.nf.test @@ -0,0 +1,106 @@ + +nextflow_process { + + name "Test Process BEAGLE5_BEAGLE" + script "../main.nf" + process "BEAGLE5_BEAGLE" + + tag "modules" + tag "modules_nfcore" + tag "beagle5" + tag "beagle5/beagle" + + test("test-beagle5-beagle") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = [] + input[4] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-beagle5-beagle-ref") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true) + ] + input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/ref.22Jul22.46e.vcf.gz", checkIfExists: true) + input[2] = [] + input[3] = [] + input[4] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-beagle5-beagle-ref-map") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true) + ] + input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/ref.22Jul22.46e.vcf.gz", checkIfExists: true) + input[2] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/plink.chr22.GRCh38.map", checkIfExists: true) + input[3] = [] + input[4] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/beagle5/beagle/tests/main.nf.test.snap b/modules/nf-core/beagle5/beagle/tests/main.nf.test.snap new file mode 100644 index 00000000000..e956af5c451 --- /dev/null +++ b/modules/nf-core/beagle5/beagle/tests/main.nf.test.snap @@ -0,0 +1,44 @@ +{ + "test-beagle5-beagle": { + "content": [ + "c64dae0a50a33b6083b8bfa0991f6eb0", + "test.bglout.log", + [ + "versions.yml:md5,d2b2dffb6ef6c2a1dd4f718a38c83a48" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:14:00.293016" + }, + "test-beagle5-beagle-ref-map": { + "content": [ + "aba50d8debbfe25cd71b50f8fd8f7ce5", + "test.bglout.log", + [ + "versions.yml:md5,d2b2dffb6ef6c2a1dd4f718a38c83a48" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:14:25.525094" + }, + "test-beagle5-beagle-ref": { + "content": [ + "bd8d96bed907d22e569746f2754f5469", + "test.bglout.log", + [ + "versions.yml:md5,d2b2dffb6ef6c2a1dd4f718a38c83a48" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:14:13.328146" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/groupby/tests/main.nf.test b/modules/nf-core/bedtools/groupby/tests/main.nf.test new file mode 100644 index 00000000000..b7dedcc2aa5 --- /dev/null +++ b/modules/nf-core/bedtools/groupby/tests/main.nf.test @@ -0,0 +1,37 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_GROUPBY" + script "../main.nf" + process "BEDTOOLS_GROUPBY" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/groupby" + + test("test-bedtools-groupby") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), + ] + input[1] = 5 + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/groupby/tests/main.nf.test.snap b/modules/nf-core/bedtools/groupby/tests/main.nf.test.snap new file mode 100644 index 00000000000..956487d0f5a --- /dev/null +++ b/modules/nf-core/bedtools/groupby/tests/main.nf.test.snap @@ -0,0 +1,37 @@ +{ + "test-bedtools-groupby": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.grouped.bed:md5,ba080b3d282f206f6312122c71a66745" + ] + ], + "1": [ + "versions.yml:md5,8f48acf848ff45a4fff4e10a806f29f5" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.grouped.bed:md5,ba080b3d282f206f6312122c71a66745" + ] + ], + "versions": [ + "versions.yml:md5,8f48acf848ff45a4fff4e10a806f29f5" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:10:16.714787" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/groupby/tests/nextflow.config b/modules/nf-core/bedtools/groupby/tests/nextflow.config new file mode 100644 index 00000000000..3b6019fb28d --- /dev/null +++ b/modules/nf-core/bedtools/groupby/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BEDTOOLS_GROUPBY { + ext.args = "-g 1" + } +} diff --git a/modules/nf-core/bedtools/jaccard/tests/main.nf.test b/modules/nf-core/bedtools/jaccard/tests/main.nf.test new file mode 100644 index 00000000000..839266b5fcc --- /dev/null +++ b/modules/nf-core/bedtools/jaccard/tests/main.nf.test @@ -0,0 +1,66 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_JACCARD" + script "../main.nf" + process "BEDTOOLS_JACCARD" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/jaccard" + + test("test-bedtools-jaccard") { + + 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) + ] + input[1] = [[],[]] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-bedtools-jaccard-genome") { + + config "./nextflow.config" + + 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) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/jaccard/tests/main.nf.test.snap b/modules/nf-core/bedtools/jaccard/tests/main.nf.test.snap new file mode 100644 index 00000000000..4783d48960f --- /dev/null +++ b/modules/nf-core/bedtools/jaccard/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-bedtools-jaccard-genome": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,b737742026a3b512a494f3aa7935fded" + ] + ], + "1": [ + "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,b737742026a3b512a494f3aa7935fded" + ] + ], + "versions": [ + "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:08:36.70775" + }, + "test-bedtools-jaccard": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,b737742026a3b512a494f3aa7935fded" + ] + ], + "1": [ + "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,b737742026a3b512a494f3aa7935fded" + ] + ], + "versions": [ + "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:08:32.019101" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/jaccard/tests/nextflow.config b/modules/nf-core/bedtools/jaccard/tests/nextflow.config new file mode 100644 index 00000000000..5208fee9b6a --- /dev/null +++ b/modules/nf-core/bedtools/jaccard/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: "BEDTOOLS_JACCARD" { + ext.args = "-sorted" + } +} diff --git a/modules/nf-core/bedtools/makewindows/tests/main.nf.test b/modules/nf-core/bedtools/makewindows/tests/main.nf.test new file mode 100644 index 00000000000..b27e59b6e04 --- /dev/null +++ b/modules/nf-core/bedtools/makewindows/tests/main.nf.test @@ -0,0 +1,58 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_MAKEWINDOWS" + script "../main.nf" + process "BEDTOOLS_MAKEWINDOWS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/makewindows" + + test("test-bedtools-makewindows-bed") { + + when { + process { + """ + input[0] = [ + [ id:'test2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-bedtools-makewindows-fai") { + + when { + process { + """ + input[0] = [ + [ id:'test2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/makewindows/tests/main.nf.test.snap b/modules/nf-core/bedtools/makewindows/tests/main.nf.test.snap new file mode 100644 index 00000000000..22cfbc17253 --- /dev/null +++ b/modules/nf-core/bedtools/makewindows/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "test-bedtools-makewindows-fai": { + "content": [ + { + "0": [ + [ + { + "id": "test2" + }, + "test2.bed:md5,622d1f62786fe4239b76c53168f21c54" + ] + ], + "1": [ + "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5" + ], + "bed": [ + [ + { + "id": "test2" + }, + "test2.bed:md5,622d1f62786fe4239b76c53168f21c54" + ] + ], + "versions": [ + "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:03:31.430455" + }, + "test-bedtools-makewindows-bed": { + "content": [ + { + "0": [ + [ + { + "id": "test2" + }, + "test2.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e" + ] + ], + "1": [ + "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5" + ], + "bed": [ + [ + { + "id": "test2" + }, + "test2.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e" + ] + ], + "versions": [ + "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:03:27.118372" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/makewindows/tests/nextflow.config b/modules/nf-core/bedtools/makewindows/tests/nextflow.config new file mode 100644 index 00000000000..fa16733f166 --- /dev/null +++ b/modules/nf-core/bedtools/makewindows/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BEDTOOLS_MAKEWINDOWS { + ext.args = '-w 50 ' + } +} diff --git a/modules/nf-core/bedtools/maskfasta/tests/main.nf.test b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test new file mode 100644 index 00000000000..14dfc33e31a --- /dev/null +++ b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test @@ -0,0 +1,35 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_MASKFASTA" + script "../main.nf" + process "BEDTOOLS_MASKFASTA" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/maskfasta" + + test("test-bedtools-maskfasta") { + + 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) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/maskfasta/tests/main.nf.test.snap b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test.snap new file mode 100644 index 00000000000..48887161bcb --- /dev/null +++ b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test-bedtools-maskfasta": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fa:md5,f4f6749698f11074228d2c79338e3b9c" + ] + ], + "1": [ + "versions.yml:md5,441689b51fc99b551e274857bb36445a" + ], + "fasta": [ + [ + { + "id": "test" + }, + "test.fa:md5,f4f6749698f11074228d2c79338e3b9c" + ] + ], + "versions": [ + "versions.yml:md5,441689b51fc99b551e274857bb36445a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:57:44.016613" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/multiinter/tests/main.nf.test b/modules/nf-core/bedtools/multiinter/tests/main.nf.test new file mode 100644 index 00000000000..ed46cf0d3bc --- /dev/null +++ b/modules/nf-core/bedtools/multiinter/tests/main.nf.test @@ -0,0 +1,65 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_MULTIINTER" + script "../main.nf" + process "BEDTOOLS_MULTIINTER" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/multiinter" + + test("test-bedtools-multiinter") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true) + ] + ] + input[1] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-bedtools-multiinter-genome") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap b/modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap new file mode 100644 index 00000000000..14cad906c41 --- /dev/null +++ b/modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-bedtools-multiinter": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7" + ] + ], + "1": [ + "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7" + ] + ], + "versions": [ + "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:55:57.797405" + }, + "test-bedtools-multiinter-genome": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7" + ] + ], + "1": [ + "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7" + ] + ], + "versions": [ + "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:56:02.192345" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/shift/tests/main.nf.test b/modules/nf-core/bedtools/shift/tests/main.nf.test new file mode 100644 index 00000000000..5c251401aea --- /dev/null +++ b/modules/nf-core/bedtools/shift/tests/main.nf.test @@ -0,0 +1,36 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_SHIFT" + script "../main.nf" + process "BEDTOOLS_SHIFT" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/shift" + + test("test-bedtools-shift") { + + when { + process { + """ + input[0] = [ [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = [[id:'sizes'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/shift/tests/main.nf.test.snap b/modules/nf-core/bedtools/shift/tests/main.nf.test.snap new file mode 100644 index 00000000000..8d5d6eba419 --- /dev/null +++ b/modules/nf-core/bedtools/shift/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test-bedtools-shift": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,fdfa2c33084f1f8e42505076a449afdc" + ] + ], + "1": [ + "versions.yml:md5,1a2d22a8a7a1de74d4316895e2d97701" + ], + "bed": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,fdfa2c33084f1f8e42505076a449afdc" + ] + ], + "versions": [ + "versions.yml:md5,1a2d22a8a7a1de74d4316895e2d97701" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:53:47.543861" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/bedtools/shift/nextflow.config b/modules/nf-core/bedtools/shift/tests/nextflow.config similarity index 52% rename from tests/modules/nf-core/bedtools/shift/nextflow.config rename to modules/nf-core/bedtools/shift/tests/nextflow.config index 19cf58773f0..229ddd6bf8b 100644 --- a/tests/modules/nf-core/bedtools/shift/nextflow.config +++ b/modules/nf-core/bedtools/shift/tests/nextflow.config @@ -1,10 +1,6 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: BEDTOOLS_SHIFT { ext.args = '-s 5' ext.prefix = { "${meta.id}_out" } } - } diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test b/modules/nf-core/bedtools/slop/tests/main.nf.test new file mode 100644 index 00000000000..c8dccc8e6ed --- /dev/null +++ b/modules/nf-core/bedtools/slop/tests/main.nf.test @@ -0,0 +1,36 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_SLOP" + script "../main.nf" + process "BEDTOOLS_SLOP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/slop" + + test("test-bedtools-slop") { + + 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.sizes', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test.snap b/modules/nf-core/bedtools/slop/tests/main.nf.test.snap new file mode 100644 index 00000000000..899ac21bac9 --- /dev/null +++ b/modules/nf-core/bedtools/slop/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test-bedtools-slop": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,4f1d8924925fe5d205c9e1981fe290a4" + ] + ], + "1": [ + "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf" + ], + "bed": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,4f1d8924925fe5d205c9e1981fe290a4" + ] + ], + "versions": [ + "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:52:04.945029" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/bedtools/slop/nextflow.config b/modules/nf-core/bedtools/slop/tests/nextflow.config similarity index 53% rename from tests/modules/nf-core/bedtools/slop/nextflow.config rename to modules/nf-core/bedtools/slop/tests/nextflow.config index 09abb51aabb..fef7548168e 100644 --- a/tests/modules/nf-core/bedtools/slop/nextflow.config +++ b/modules/nf-core/bedtools/slop/tests/nextflow.config @@ -1,10 +1,6 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: BEDTOOLS_SLOP { ext.args = '-l 15 -r 30' ext.prefix = { "${meta.id}_out" } } - } diff --git a/modules/nf-core/bedtools/split/tests/main.nf.test b/modules/nf-core/bedtools/split/tests/main.nf.test new file mode 100644 index 00000000000..a59891b7936 --- /dev/null +++ b/modules/nf-core/bedtools/split/tests/main.nf.test @@ -0,0 +1,36 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_SPLIT" + script "../main.nf" + process "BEDTOOLS_SPLIT" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/split" + + test("test-bedtools-split") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true), + 2 + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/split/tests/main.nf.test.snap b/modules/nf-core/bedtools/split/tests/main.nf.test.snap new file mode 100644 index 00000000000..359b3aa93b7 --- /dev/null +++ b/modules/nf-core/bedtools/split/tests/main.nf.test.snap @@ -0,0 +1,41 @@ +{ + "test-bedtools-split": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test.00001.bed:md5,d58e5e46c2fcc3b8be5db0f023e93cb5", + "test.00002.bed:md5,03caf952e9297a54620d2bbba8dc2823" + ] + ] + ], + "1": [ + "versions.yml:md5,33e0d5f886b7f0ed6f9c3e19b049357f" + ], + "beds": [ + [ + { + "id": "test" + }, + [ + "test.00001.bed:md5,d58e5e46c2fcc3b8be5db0f023e93cb5", + "test.00002.bed:md5,03caf952e9297a54620d2bbba8dc2823" + ] + ] + ], + "versions": [ + "versions.yml:md5,33e0d5f886b7f0ed6f9c3e19b049357f" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:50:28.137857" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/subtract/tests/main.nf.test b/modules/nf-core/bedtools/subtract/tests/main.nf.test new file mode 100644 index 00000000000..cc4729c8bf2 --- /dev/null +++ b/modules/nf-core/bedtools/subtract/tests/main.nf.test @@ -0,0 +1,36 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_SUBTRACT" + script "../main.nf" + process "BEDTOOLS_SUBTRACT" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/subtract" + + test("test-bedtools-subtract") { + + when { + process { + """ + input[0] = [ + [ id:'test_subtract' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/subtract/tests/main.nf.test.snap b/modules/nf-core/bedtools/subtract/tests/main.nf.test.snap new file mode 100644 index 00000000000..1dc0e6e7464 --- /dev/null +++ b/modules/nf-core/bedtools/subtract/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test-bedtools-subtract": { + "content": [ + { + "0": [ + [ + { + "id": "test_subtract" + }, + "test_subtract.bed:md5,63513c4dc69e8b481ce3b4b2a9f24259" + ] + ], + "1": [ + "versions.yml:md5,1424765d0d00cc3f44f5e7745607effe" + ], + "bed": [ + [ + { + "id": "test_subtract" + }, + "test_subtract.bed:md5,63513c4dc69e8b481ce3b4b2a9f24259" + ] + ], + "versions": [ + "versions.yml:md5,1424765d0d00cc3f44f5e7745607effe" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:47:34.662548" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test new file mode 100644 index 00000000000..8d22aabdcfc --- /dev/null +++ b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test @@ -0,0 +1,56 @@ + +nextflow_process { + + name "Test Process GATK_UNIFIEDGENOTYPER" + script "../main.nf" + process "GATK_UNIFIEDGENOTYPER" + + tag "modules" + tag "modules_nfcore" + tag "gatk" + tag "gatk/unifiedgenotyper" + + test("test-gatk-unifiedgenotyper") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input[1] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + input[6] = [[],[]] + input[7] = [[],[]] + + """ + } + } + + 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/gatk/unifiedgenotyper/tests/main.nf.test.snap b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test.snap new file mode 100644 index 00000000000..51c93dc5e63 --- /dev/null +++ b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-gatk-unifiedgenotyper": { + "content": [ + "577c77d9323f6256931a6846eaac3f40", + [ + "versions.yml:md5,f0dfc5a0252a665c12a2b27444f73e67" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:30:01.119639" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test new file mode 100644 index 00000000000..f06292f2eed --- /dev/null +++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test @@ -0,0 +1,137 @@ + +nextflow_process { + + name "Test Process GATK4_CALIBRATEDRAGSTRMODEL" + script "../main.nf" + process "GATK4_CALIBRATEDRAGSTRMODEL" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/calibratedragstrmodel" + + test("test-gatk4-calibratedragstrmodel-bam") { + + 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), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.dragstr_model[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-calibratedragstrmodel-cram") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.dragstr_model[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-calibratedragstrmodel-beds") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.dragstr_model[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-calibratedragstrmodel-gzipped-beds") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.dragstr_model[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap new file mode 100644 index 00000000000..d0d7b8b9dce --- /dev/null +++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap @@ -0,0 +1,78 @@ +{ + "test-gatk4-calibratedragstrmodel-bam": { + "content": [ + [ + "# sample = testN", + "# readGroups = 1", + "# estimatedOrDefaults = defaults", + "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.bam --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false", + "############################################################################################" + ], + [ + "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:22:17.584362" + }, + "test-gatk4-calibratedragstrmodel-cram": { + "content": [ + [ + "# sample = testN", + "# readGroups = 1", + "# estimatedOrDefaults = defaults", + "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false", + "############################################################################################" + ], + [ + "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:22:30.21551" + }, + "test-gatk4-calibratedragstrmodel-gzipped-beds": { + "content": [ + [ + "# sample = testN", + "# readGroups = 1", + "# estimatedOrDefaults = defaults", + "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false", + "############################################################################################" + ], + [ + "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:22:53.619871" + }, + "test-gatk4-calibratedragstrmodel-beds": { + "content": [ + [ + "# sample = testN", + "# readGroups = 1", + "# estimatedOrDefaults = defaults", + "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false", + "############################################################################################" + ], + [ + "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:22:41.938548" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test new file mode 100644 index 00000000000..0832cf85a24 --- /dev/null +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test @@ -0,0 +1,104 @@ + +nextflow_process { + + name "Test Process GATK4_COLLECTREADCOUNTS" + script "../main.nf" + process "GATK4_COLLECTREADCOUNTS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectreadcounts" + + test("test-gatk4-collectreadcounts-hdf5") { + + config "./nextflow.hdf5.config" + + 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), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.hdf5[0][1]).name, + process.out.tsv, + ).match() + } + ) + } + } + + test("test-gatk4-collectreadcounts-tsv") { + + config "./nextflow.tsv.config" + + 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), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-gatk4-collectreadcounts-cram") { + + config "./nextflow.cram.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + ] + input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)] + input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)] + input[3] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap new file mode 100644 index 00000000000..28a3a6e151b --- /dev/null +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap @@ -0,0 +1,97 @@ +{ + "test-gatk4-collectreadcounts-cram": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d9a32039b7a84f5bb74e8382e5427670" + ] + ], + "2": [ + "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + ], + "hdf5": [ + + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d9a32039b7a84f5bb74e8382e5427670" + ] + ], + "versions": [ + "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:58:19.610687" + }, + "test-gatk4-collectreadcounts-hdf5": { + "content": [ + "test.hdf5", + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:02:48.607644" + }, + "test-gatk4-collectreadcounts-tsv": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,8e45a6164916c303387f39f02ce45841" + ] + ], + "2": [ + "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + ], + "hdf5": [ + + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,8e45a6164916c303387f39f02ce45841" + ] + ], + "versions": [ + "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:58:07.500024" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.cram.config b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.cram.config new file mode 100644 index 00000000000..682bdcad1e5 --- /dev/null +++ b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.cram.config @@ -0,0 +1,5 @@ +process { + withName: 'GATK4_COLLECTREADCOUNTS' { + ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" + } +} diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.hdf5.config b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.hdf5.config new file mode 100644 index 00000000000..d6ca881b7e3 --- /dev/null +++ b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.hdf5.config @@ -0,0 +1,5 @@ +process { + withName: 'GATK4_COLLECTREADCOUNTS'{ + ext.args = "--interval-merging-rule OVERLAPPING_ONLY" + } +} diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.tsv.config b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.tsv.config new file mode 100644 index 00000000000..682bdcad1e5 --- /dev/null +++ b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.tsv.config @@ -0,0 +1,5 @@ +process { + withName: 'GATK4_COLLECTREADCOUNTS' { + ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" + } +} diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test new file mode 100644 index 00000000000..308fc7f678e --- /dev/null +++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test @@ -0,0 +1,121 @@ + +nextflow_process { + + name "Test Process GATK4_COLLECTSVEVIDENCE" + script "../main.nf" + process "GATK4_COLLECTSVEVIDENCE" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectsvevidence" + + test("test-gatk4-collectsvevidence-cram") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + [], + [] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.split_read_evidence[0][1]).linesGzip[0], + file(process.out.split_read_evidence_index[0][1]).name, + path(process.out.paired_end_evidence[0][1]).linesGzip[0], + file(process.out.paired_end_evidence_index[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-collectsvevidence-bam") { + + 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), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [], + [] + ] + input[1] = [] + input[2] = [] + input[3] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.split_read_evidence[0][1]).linesGzip[0], + file(process.out.split_read_evidence_index[0][1]).name, + path(process.out.paired_end_evidence[0][1]).linesGzip[0], + file(process.out.paired_end_evidence_index[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-collectsvevidence-allele-count") { + + 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), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.split_read_evidence[0][1]).linesGzip[0], + file(process.out.split_read_evidence_index[0][1]).name, + path(process.out.paired_end_evidence[0][1]).linesGzip[0], + file(process.out.paired_end_evidence_index[0][1]).name, + path(process.out.site_depths[0][1]).linesGzip[0], + file(process.out.site_depths_index[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap new file mode 100644 index 00000000000..5143cf3c0be --- /dev/null +++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap @@ -0,0 +1,52 @@ +{ + "test-gatk4-collectsvevidence-cram": { + "content": [ + "chr22\t2008\tleft\t1\tnormal", + "test.sr.txt.gz.tbi", + "chr22\t3320\t+\tchr22\t3482\t-\tnormal", + "test.pe.txt.gz.tbi", + [ + "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:51:11.44656" + }, + "test-gatk4-collectsvevidence-allele-count": { + "content": [ + "chr22\t2008\tleft\t1\tnormal", + "test.sr.txt.gz.tbi", + "chr22\t3320\t+\tchr22\t3482\t-\tnormal", + "test.pe.txt.gz.tbi", + "chr22\t1981\tnormal\t235\t0\t48\t0", + "test.sd.txt.gz.tbi", + [ + "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:48:13.663238" + }, + "test-gatk4-collectsvevidence-bam": { + "content": [ + "chr22\t2008\tleft\t1\tnormal", + "test.sr.txt.gz.tbi", + "chr22\t3320\t+\tchr22\t3482\t-\tnormal", + "test.pe.txt.gz.tbi", + [ + "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:51:22.087808" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/nextflow.config b/modules/nf-core/gatk4/collectsvevidence/tests/nextflow.config new file mode 100644 index 00000000000..ca7c056227f --- /dev/null +++ b/modules/nf-core/gatk4/collectsvevidence/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GATK4_COLLECTSVEVIDENCE { + ext.args = "--sample-name normal" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test new file mode 100644 index 00000000000..7d066cf1ffb --- /dev/null +++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test @@ -0,0 +1,38 @@ + +nextflow_process { + + name "Test Process GATK4_COMPOSESTRTABLEFILE" + script "../main.nf" + process "GATK4_COMPOSESTRTABLEFILE" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/composestrtablefile" + + test("test-gatk4-composestrtablefile") { + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.str_table[0]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap new file mode 100644 index 00000000000..02136a8b365 --- /dev/null +++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-gatk4-composestrtablefile": { + "content": [ + "genome.zip", + [ + "versions.yml:md5,755f9a44a99148151b624d70eb6ce260" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:37:10.366333" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test new file mode 100644 index 00000000000..0f65f542891 --- /dev/null +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test @@ -0,0 +1,44 @@ + +nextflow_process { + + name "Test Process GATK4_CONDENSEDEPTHEVIDENCE" + script "../main.nf" + process "GATK4_CONDENSEDEPTHEVIDENCE" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/condensedepthevidence" + + test("test-gatk4-condensdepthevidence") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz.tbi", checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.condensed_evidence[0][1]).linesGzip[0..1], + file(process.out.condensed_evidence_index[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap new file mode 100644 index 00000000000..d8da0978b2b --- /dev/null +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap @@ -0,0 +1,19 @@ +{ + "test-gatk4-condensdepthevidence": { + "content": [ + [ + "#Chr\tStart\tEnd\ttestN", + "chr22\t0\t40001\t5642" + ], + "test.rd.txt.gz.tbi", + [ + "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:33:21.910858" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test new file mode 100644 index 00000000000..2e3688a779d --- /dev/null +++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test @@ -0,0 +1,64 @@ + +nextflow_process { + + name "Test Process GATK4_FASTQTOSAM" + script "../main.nf" + process "GATK4_FASTQTOSAM" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/fastqtosam" + + test("test-gatk4-fastqtosam-single-end") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-fastqtosam-paired-end") { + + when { + process { + """ + input[0] = [ [ 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) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap new file mode 100644 index 00000000000..554480a24b7 --- /dev/null +++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap @@ -0,0 +1,28 @@ +{ + "test-gatk4-fastqtosam-single-end": { + "content": [ + "e6a4aa204d980e177a0458596f0a70ac", + [ + "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:29:12.362942" + }, + "test-gatk4-fastqtosam-paired-end": { + "content": [ + "e6a4aa204d980e177a0458596f0a70ac", + [ + "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:29:22.385798" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test new file mode 100644 index 00000000000..a84f562e394 --- /dev/null +++ b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test @@ -0,0 +1,38 @@ + +nextflow_process { + + name "Test Process GATK4_FILTERINTERVALS" + script "../main.nf" + process "GATK4_FILTERINTERVALS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/filterintervals" + + test("test-gatk4-filterintervals") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list', checkIfExists: true) + ] + input[1] = [ [:], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv', checkIfExists: true) ] ] + input[2] = [ [:], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.annotated_intervals.tsv', checkIfExists: true) ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap new file mode 100644 index 00000000000..c9626666948 --- /dev/null +++ b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test-gatk4-filterintervals": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,67b15dff732693db3542e6b1dc30a5da" + ] + ], + "1": [ + "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30" + ], + "interval_list": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,67b15dff732693db3542e6b1dc30a5da" + ] + ], + "versions": [ + "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:25:35.933532" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/filterintervals/nextflow.config b/modules/nf-core/gatk4/filterintervals/tests/nextflow.config similarity index 51% rename from tests/modules/nf-core/gatk4/filterintervals/nextflow.config rename to modules/nf-core/gatk4/filterintervals/tests/nextflow.config index 7cdcd35fb86..93ea379c8d4 100644 --- a/tests/modules/nf-core/gatk4/filterintervals/nextflow.config +++ b/modules/nf-core/gatk4/filterintervals/tests/nextflow.config @@ -1,9 +1,5 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: GATK4_FILTERINTERVALS { ext.args = "--interval-merging-rule OVERLAPPING_ONLY" } - } \ No newline at end of file diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test new file mode 100644 index 00000000000..173b149b547 --- /dev/null +++ b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test @@ -0,0 +1,60 @@ + +nextflow_process { + + name "Test Process GATK4_GATHERBQSRREPORTS" + script "../main.nf" + process "GATK4_GATHERBQSRREPORTS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/gatherbqsrreports" + + test("test-gatk4-gatherbqsrreports") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-gatk4-gatherbqsrreports-multiple") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table', checkIfExists: true) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap new file mode 100644 index 00000000000..bc5d4bd1332 --- /dev/null +++ b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-gatk4-gatherbqsrreports-multiple": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.table:md5,0c1257eececf95db8ca378272d0f21f9" + ] + ], + "1": [ + "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + ], + "table": [ + [ + { + "id": "test", + "single_end": false + }, + "test.table:md5,0c1257eececf95db8ca378272d0f21f9" + ] + ], + "versions": [ + "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:22:34.490694" + }, + "test-gatk4-gatherbqsrreports": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.table:md5,9603b69fdc3b5090de2e0dd78bfcc4bf" + ] + ], + "1": [ + "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + ], + "table": [ + [ + { + "id": "test", + "single_end": false + }, + "test.table:md5,9603b69fdc3b5090de2e0dd78bfcc4bf" + ] + ], + "versions": [ + "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:22:10.552951" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index 561e9bb8b88..c784d59ab26 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -14,7 +14,7 @@ process GATK4_GATHERPILEUPSUMMARIES { output: tuple val(meta), path("*.pileups.table"), emit: table - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test new file mode 100644 index 00000000000..8497e64db37 --- /dev/null +++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test @@ -0,0 +1,37 @@ + +nextflow_process { + + name "Test Process GATK4_GATHERPILEUPSUMMARIES" + script "../main.nf" + process "GATK4_GATHERPILEUPSUMMARIES" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/gatherpileupsummaries" + + test("test-gatk4-gatherpileupsummaries") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap new file mode 100644 index 00000000000..f05a7ef0d11 --- /dev/null +++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap @@ -0,0 +1,37 @@ +{ + "test-gatk4-gatherpileupsummaries": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.out.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + ] + ], + "1": [ + "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + ], + "table": [ + [ + { + "id": "test", + "single_end": false + }, + "test.out.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + ] + ], + "versions": [ + "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:18:40.835226" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config b/modules/nf-core/gatk4/gatherpileupsummaries/tests/nextflow.config similarity index 51% rename from tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config rename to modules/nf-core/gatk4/gatherpileupsummaries/tests/nextflow.config index 48afc706e6c..2b49a6fa39d 100644 --- a/tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config +++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/nextflow.config @@ -1,7 +1,4 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'GATK4_GATHERPILEUPSUMMARIES' { ext.prefix = { "${meta.id}.out" } } diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test new file mode 100644 index 00000000000..bffe02e4f6c --- /dev/null +++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test @@ -0,0 +1,38 @@ + +nextflow_process { + + name "Test Process GATK4_LEARNREADORIENTATIONMODEL" + script "../main.nf" + process "GATK4_LEARNREADORIENTATIONMODEL" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/learnreadorientationmodel" + + test("test-gatk4-learnreadorientationmodel") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz', checkIfExists: true)] ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.artifactprior[0][1]).linesGzip[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap new file mode 100644 index 00000000000..b829bd9c4aa --- /dev/null +++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "test-gatk4-learnreadorientationmodel": { + "content": [ + [ + "CTT\tAAG\t2.7114986684474486E-6\t3.2076972826656866E-5\t2.6085822355549755E-6\t0.0\t2.6371799896540086E-6\t3.3869355267901446E-6\t2.6085822355549755E-6\t0.0\t0.9995881552107633\t4.6590850211691583E-5\t2.8848017683240004E-4\t3.0744010710100574E-5\t38334\t116", + "GTT\tAAC\t0.1\t0.1\t0.1\t0.0\t0.1\t0.1\t0.1\t0.0\t0.1\t0.1\t0.1\t0.1\t0\t0", + "TAT\tATA\t0.0\t5.548307163536064E-6\t5.144357865084592E-6\t6.205892051757818E-6\t0.0\t5.907388162200423E-6\t5.176730417709638E-6\t6.083872804985981E-6\t0.9924019419831304\t3.946972069386949E-5\t0.007516612822150651\t7.908925559851714E-6\t19439\t95", + "AAA\tTTT\t0.0\t1.7634470563520664E-6\t2.8327478284981175E-6\t1.8084237600021914E-6\t0.0\t1.7692606885284446E-6\t2.263339968296726E-6\t1.8660094002474611E-6\t0.9990845693211764\t1.8004690536795885E-5\t8.701192700921183E-4\t1.5003489492700572E-5\t56708\t130", + "CAA\tTTG\t0.0\t3.4445551925564533E-6\t3.435193155024585E-6\t5.139879646597498E-6\t0.0\t3.4674461103560476E-6\t3.428570449688764E-6\t6.343168047383713E-6\t0.9945238954147358\t1.3629167993931722E-4\t0.0052793454402581125\t3.5208652465150646E-5\t29263\t197" + ], + [ + "versions.yml:md5,88928ff140a0967e574e66944fd2a2f2" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:16:08.296564" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config b/modules/nf-core/gatk4/learnreadorientationmodel/tests/nextflow.config similarity index 52% rename from tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config rename to modules/nf-core/gatk4/learnreadorientationmodel/tests/nextflow.config index 463e2d54932..79e4f67df3e 100644 --- a/tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config +++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/nextflow.config @@ -1,9 +1,5 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: GATK4_LEARNREADORIENTATIONMODEL { ext.prefix = { "${meta.id}.artifact-prior" } } - } diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test new file mode 100644 index 00000000000..581d730e5ac --- /dev/null +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test @@ -0,0 +1,76 @@ + +nextflow_process { + + name "Test Process GATK4_LEFTALIGNANDTRIMVARIANTS" + script "../main.nf" + process "GATK4_LEFTALIGNANDTRIMVARIANTS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/leftalignandtrimvariants" + + test("test-gatk4-leftalignandtrimvariants-interval") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // 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/test.vcf.gz.tbi', checkIfExists: true), + 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.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.summary, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-leftalignandtrimvariants-no-interval") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // 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/test.vcf.gz.tbi', 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.dict', 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() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap new file mode 100644 index 00000000000..f500c0dcc08 --- /dev/null +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap @@ -0,0 +1,30 @@ +{ + "test-gatk4-leftalignandtrimvariants-no-interval": { + "content": [ + "85745045e9c55d3846d80bfde08a7d34", + "test.normalised.vcf.gz.tbi", + [ + "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:09:35.03744" + }, + "test-gatk4-leftalignandtrimvariants-interval": { + "content": [ + "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]", + "test.normalised.vcf.gz.tbi", + [ + "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:11:42.893725" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/nextflow.config similarity index 65% rename from tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config rename to modules/nf-core/gatk4/leftalignandtrimvariants/tests/nextflow.config index 56fcee59a9a..dfe16334636 100644 --- a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/nextflow.config @@ -1,7 +1,4 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'GATK4_LEFTALIGNANDTRIMVARIANTS' { ext.args = "--split-multi-allelics --dont-trim-alleles --keep-original-ac" ext.prefix = { "${meta.id}.normalised" } diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test new file mode 100644 index 00000000000..96e93bb1995 --- /dev/null +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test @@ -0,0 +1,73 @@ + +nextflow_process { + + name "Test Process GATK4_MERGEBAMALIGNMENT" + script "../main.nf" + process "GATK4_MERGEBAMALIGNMENT" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/mergebamalignment" + + test("test-gatk4-mergebamalignment") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-mergebamalignment-stubs") { + options '-stub' + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap new file mode 100644 index 00000000000..719a7bb3311 --- /dev/null +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "test-gatk4-mergebamalignment-stubs": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:02:15.41024" + }, + "test-gatk4-mergebamalignment": { + "content": [ + "30c325e1e032eb1782a280d34c0fb1c7", + [ + "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:02:08.379035" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test new file mode 100644 index 00000000000..a546fac5aa3 --- /dev/null +++ b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test @@ -0,0 +1,49 @@ + +nextflow_process { + + name "Test Process GATK4_PREPROCESSINTERVALS" + script "../main.nf" + process "GATK4_PREPROCESSINTERVALS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/preprocessintervals" + + test("test-gatk4-preprocessintervals") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[1] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[2] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[3] = [[],[]] + input[4] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.blacklist_intervals.bed', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap new file mode 100644 index 00000000000..5365291dab8 --- /dev/null +++ b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test-gatk4-preprocessintervals": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,ce14b8fb47a60483fe44473ba40e1583" + ] + ], + "1": [ + "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4" + ], + "interval_list": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,ce14b8fb47a60483fe44473ba40e1583" + ] + ], + "versions": [ + "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T11:58:51.314382" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config b/modules/nf-core/gatk4/preprocessintervals/tests/nextflow.config similarity index 53% rename from tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config rename to modules/nf-core/gatk4/preprocessintervals/tests/nextflow.config index b1fa3d68db9..a53707fb36a 100644 --- a/tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config +++ b/modules/nf-core/gatk4/preprocessintervals/tests/nextflow.config @@ -1,9 +1,5 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: GATK4_PREPROCESSINTERVALS { ext.args = "--padding 0 --interval-merging-rule OVERLAPPING_ONLY" } - } \ No newline at end of file diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test b/modules/nf-core/gatk4/printreads/tests/main.nf.test new file mode 100644 index 00000000000..c0788619700 --- /dev/null +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test @@ -0,0 +1,95 @@ + +nextflow_process { + + name "Test Process GATK4_PRINTREADS" + script "../main.nf" + process "GATK4_PRINTREADS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/printreads" + + test("test-gatk4-printreads-bam") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + + input[1] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + input[2] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + + input[3] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.cram, + process.out.sam, + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-printreads-cram") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ] + + input[1] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + + input[2] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + + input[3] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam, + bam(process.out.cram[0][1]).getHeaderMD5(), + process.out.sam, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap new file mode 100644 index 00000000000..7f1266f2641 --- /dev/null +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap @@ -0,0 +1,40 @@ +{ + "test-gatk4-printreads-bam": { + "content": [ + "894549ee3ced6b5ca2eed2563a985217", + [ + + ], + [ + + ], + [ + "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T11:48:53.871683" + }, + "test-gatk4-printreads-cram": { + "content": [ + [ + + ], + "591299d00e262474250c5ccc241bba59", + [ + + ], + [ + "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:42:29.968056" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test b/modules/nf-core/gatk4/revertsam/tests/main.nf.test new file mode 100644 index 00000000000..b5268048587 --- /dev/null +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test @@ -0,0 +1,59 @@ + +nextflow_process { + + name "Test Process GATK4_REVERTSAM" + script "../main.nf" + process "GATK4_REVERTSAM" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/revertsam" + + test("test-gatk4-revertsam") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-revertsam-stubs") { + options '-stub' + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap new file mode 100644 index 00000000000..1cbb5ce6e79 --- /dev/null +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "test-gatk4-revertsam": { + "content": [ + "e3cfa46b13cc4fc425cccae944f43b10", + [ + "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T11:45:39.712635" + }, + "test-gatk4-revertsam-stubs": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.reverted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + ], + "bam": [ + [ + { + "id": "test" + }, + "test.reverted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T11:45:46.856318" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test new file mode 100644 index 00000000000..30a41adddf6 --- /dev/null +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test @@ -0,0 +1,88 @@ + +nextflow_process { + + name "Test Process GATK4_SAMTOFASTQ" + script "../main.nf" + process "GATK4_SAMTOFASTQ" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/samtofastq" + + test("test-gatk4-samtofastq-single-end") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end: true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.fastq[0][1]).linesGzip[3..7], + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-samtofastq-paired-end") { + + 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) ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fastq[0][1].collect { path(it).linesGzip[3..7] }, + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-samtofastq-paired-end-stubs") { + options '-stub' + when { + process { + """ + input[0] = [ [ id:'test', single_end: true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fastq[0][1].collect { file(it).name }, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap new file mode 100644 index 00000000000..0e1ec4b79d4 --- /dev/null +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap @@ -0,0 +1,66 @@ +{ + "test-gatk4-samtofastq-single-end": { + "content": [ + [ + 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"m64014_190506_005857/9307762/ccs\tlde_pass\tchr22:16600000-16800000\t169225\t199436\t+\t2\t0\t0>3\t0,0,0,0,0>2,0,1,0,0\t0>2M_2.A.C_1M_2I\t__________>__X_II____\t3S4=1X23=3X26=1X3=1X19=1X27=1X14=1X30=1X10=1X40=1X10=1X1=1X26=1X5=1X28=1X60=1X7=1X5=1X6=1X50=1X32=1X11=1X41=1X52=1X41=1X1=1X20=1X32=1X10=1X17=1X51=1X40=1X6=1X16=1X43=1X19=1X37=1X8=1X11=1X4=1X33=1X7=1X34=1X4=1X2=1X47=1X7=2X11=1X2=1X5=1X6=1X26=1X14=1X9=1X23=1X12=1X27=1X10=1X28=1X8=1X8=1X3=1X47=1X16=1X16=1X28=1X31=1X4=1X3=1X36=1X2=1X36=1X29=1X4=1X37=2X1=2X2=1X12=1X19=1X75=1X26=2D11=1X8=1X15=1X1=1X14=1X18=1X1=1X7=1X14=1X22=1X30=1X4=1X15=1X9=1X71=2X25=1X17=1X17=1X17=1X28=4D21=1X8=1X16=1X140=1X43=1X51=1X14=1X11=1X17=2X15=1X24=1X25=1X7=1X2=1X8=1X5=1X4=1X15=1X11=1X18=1D42=1X19=1X5=1X7=1X15=9D5=4D18=1X3=1X4=1X17=1X7=1X1=1X17=1X7=1X11=1X4=1X4=1X14=1X11=1X8=1X2=1X4=1X11=1X13=1X10=1X8=1X17=27297N2=1X1=2I22=8S" + ], + "cluster_id\ttrans_id\tstrand\ta_percent\ta_count\tsequence", + [ + "m64014_190506_005857/13631523/ccs\tchimeric\tchimeric\tNA\tNA\tNA\tNA\tNA", + "m64014_190506_005857/13238379/ccs\tforward_strand\tdiscarded\t7.53\t6.24\t0;3600;8;2;40\t3893\t2807S12=1X2=1D2=2X5=1X7=2X5=2I2=5I1X6=1X6=1X17=2X6=1X7=1X2=1X6=1X1=1X9=2X7=1X3=1X6=2X7=1X1=1X3=3030N1=2X12=1X17=2X4=1I7=1X5=1X8=1X25=1X5=1X2=1D8=1X12=1X1=2X9=2X7=793S", + "m64014_190506_005857/5048548/ccs\tnot_primary\tnot_primary\tNA\tNA\tNA\tNA\tNA", + "m64014_190506_005857/2491688/ccs\tchimeric\tchimeric\tNA\tNA\tNA\tNA\tNA", + "m64014_190506_005857/10945888/ccs\tnot_primary\tnot_primary\tNA\tNA\tNA\tNA\tNA" + ], + "read_id\tscaff_name\tstart_pos\tcigar\tstrands", + [ + "G1.3\t1\t99.21\t99.21\t92.96\t92.96\t0\t0\t0\t0\tna", + "G1.4\t1\t99.31\t99.31\t93.56\t93.56\t0\t0\t0\t0\tna", + "G1.5\t1\t99.69\t99.69\t95.46\t95.46\t0,0\t0,0\t0,0\t0,0\t0>0", + "G1.6\t1\t99.74\t99.74\t93.58\t93.58\t0,0\t0,0\t0,0\t0,0\t4.T.A_3M>0", + "G1.7\t1\t99.62\t99.62\t93.7\t93.7\t0,0\t0,0\t0,0\t0,0\t0>2M_2.A.C_1M_2I" + ], + [ + "chr22:16600000-16800000_6225\tm64014_190506_005857/11141276/ccs,m64014_190506_005857/13501955/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/7211438/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/9045622/ccs,m64014_190506_005857/9896837/ccs", + "chr22:16600000-16800000_6234\tm64014_190506_005857/10945789/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/9045622/ccs,m64014_190506_005857/9896837/ccs", + "chr22:16600000-16800000_6244\tm64014_190506_005857/10945789/ccs,m64014_190506_005857/11141276/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13501955/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/9045622/ccs,m64014_190506_005857/9896837/ccs", + "chr22:16600000-16800000_6255\tm64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/9896837/ccs", + "chr22:16600000-16800000_6256\tm64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13501955/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/9896837/ccs" + ], + [ + "chr22:16600000-16800000\t6225\tM\tT\tC\t8\t8\tm64014_190506_005857/9045622/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/11141276/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/7211438/ccs,m64014_190506_005857/13501955/ccs", + "chr22:16600000-16800000\t6234\tM\tG\tA\t5\t7\tm64014_190506_005857/9896837/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/9045622/ccs", + "chr22:16600000-16800000\t6244\tM\tC\tG\t11\t12\tm64014_190506_005857/9045622/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/11141276/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/10945789/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/13501955/ccs", + "chr22:16600000-16800000\t6255\tM\tT\tC\t7\t7\tm64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/3735911/ccs", + "chr22:16600000-16800000\t6256\tM\tG\tA\t7\t8\tm64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/3735911/ccs" + ], + [ + "versions.yml:md5,e78d77df56e6434d307e702b7875d005" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:53:08.268377" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gstama/collapse/nextflow.config b/modules/nf-core/gstama/collapse/tests/nextflow.config similarity index 54% rename from tests/modules/nf-core/gstama/collapse/nextflow.config rename to modules/nf-core/gstama/collapse/tests/nextflow.config index a68f33f2ea0..ea89a16473c 100644 --- a/tests/modules/nf-core/gstama/collapse/nextflow.config +++ b/modules/nf-core/gstama/collapse/tests/nextflow.config @@ -1,10 +1,6 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: GSTAMA_COLLAPSE { ext.args = '-x capped -b BAM' ext.prefix = { "${meta.id}_tc" } } - } diff --git a/modules/nf-core/gstama/merge/tests/main.nf.test b/modules/nf-core/gstama/merge/tests/main.nf.test new file mode 100644 index 00000000000..c485d3eaafa --- /dev/null +++ b/modules/nf-core/gstama/merge/tests/main.nf.test @@ -0,0 +1,47 @@ + +nextflow_process { + + name "Test Process GSTAMA_MERGE" + script "../main.nf" + process "GSTAMA_MERGE" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gstama" + tag "gstama/merge" + + test("test-gstama-merge") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/txt/filelist.txt', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bed, + file(process.out.gene_report[0][1]).readLines()[3..7], + file(process.out.merge[0][1]).readLines()[3..7], + file(process.out.trans_report[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gstama/merge/tests/main.nf.test.snap b/modules/nf-core/gstama/merge/tests/main.nf.test.snap new file mode 100644 index 00000000000..0ac82c39e0f --- /dev/null +++ b/modules/nf-core/gstama/merge/tests/main.nf.test.snap @@ -0,0 +1,44 @@ +{ + "test-gstama-merge": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_merged.bed:md5,60ec34e1ff9655d4ce2e83d3f4bbf448" + ] + ], + [ + "G3\t1\t1\tGM2\t22\t16154707\t16159526\tGM2_G2\tGM2:1", + "G4\t1\t1\tGM2\t22\t19520556\t19524409\tGM2_G3\tGM2:1", + "G5\t3\t3\tGM2\t22\t20675820\t20834631\tGM2_G4\tGM2:1", + "G6\t1\t1\tGM2\t22\t21927942\t21952850\tGM2_G5\tGM2:1", + "G7\t1\t1\tGM2\t22\t23226655\t23231517\tGM2_G6\tGM2:1" + ], + [ + "22\t11867751\t11883593\tG2.1;GM2_G1.1\t40\t+\t11867751\t11883593\t255,0,0\t5\t2147,85,29,73,1326\t0,6089,8352,8472,14516", + "22\t16154707\t16159526\tG3.1;GM2_G2.1\t40\t+\t16154707\t16159526\t255,0,0\t1\t4819\t0", + "22\t19520556\t19524409\tG4.1;GM2_G3.1\t40\t-\t19520556\t19524409\t255,0,0\t1\t3853\t0", + "22\t20675820\t20726523\tG5.1;GM2_G4.1\t40\t-\t20675820\t20726523\t255,0,0\t15\t22,399,84,90,160,121,126,105,110,71,73,71,130,121,36\t0,31879,33475,34087,34878,35520,36665,36872,37460,38637,38807,41887,42872,45477,50667", + "22\t20707690\t20834631\tG5.2;GM2_G4.2\t40\t-\t20707690\t20834631\t255,0,0\t53\t408,84,90,160,121,126,105,110,71,73,71,130,121,54,168,91,194,80,120,128,108,152,159,128,157,93,120,90,84,82,125,71,83,134,137,109,51,169,104,184,96,133,130,101,192,97,66,149,67,260,73,89,70\t0,1605,2217,3008,3650,4795,5002,5590,6767,6937,10017,11002,13607,18797,19539,20083,21622,21941,22201,25280,26045,26352,26704,34537,34917,36937,39892,42214,43602,43983,45212,45419,53613,57126,57409,57894,85502,88455,90893,91402,91980,94282,95500,96609,97283,99671,103276,105667,110792,111950,112848,116635,126871" + ], + [ + "G1.3\t1\tGM1\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\tGM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2\tGM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2\tGM1_G1.2", + "G2.1\t1\tGM2\t0,0,0,0,0\t0,0,0,0,0\tGM2_G1.1;GM2_G1.1;GM2_G1.1;GM2_G1.1;GM2_G1.1\tGM2_G1.1;GM2_G1.1;GM2_G1.1;GM2_G1.1;GM2_G1.1\tGM2_G1.1", + "G3.1\t1\tGM2\t0\t0\tGM2_G2.1\tGM2_G2.1\tGM2_G2.1", + "G4.1\t1\tGM2\t0\t0\tGM2_G3.1\tGM2_G3.1\tGM2_G3.1", + "G5.1\t1\tGM2\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\tGM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1\tGM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1\tGM2_G4.1" + ], + [ + "versions.yml:md5,ceaccf17d15e3fabb193d67b4a822d08" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:46:55.890773" + } +} \ No newline at end of file diff --git a/modules/nf-core/gstama/merge/tests/nextflow.config b/modules/nf-core/gstama/merge/tests/nextflow.config new file mode 100644 index 00000000000..02d0a81e0d3 --- /dev/null +++ b/modules/nf-core/gstama/merge/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GSTAMA_MERGE { + ext.prefix = { "${meta.id}_merged" } + } +} diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test new file mode 100644 index 00000000000..c447f001dc0 --- /dev/null +++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test @@ -0,0 +1,42 @@ + +nextflow_process { + + name "Test Process GSTAMA_POLYACLEANUP" + script "../main.nf" + process "GSTAMA_POLYACLEANUP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gstama" + tag "gstama/polyacleanup" + + test("test-gstama-polyacleanup") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.report[0][1]).linesGzip[0..2], + path(process.out.fasta[0][1]).linesGzip[3..7], + path(process.out.tails[0][1]).linesGzip[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap new file mode 100644 index 00000000000..a9cc2aefef1 --- /dev/null +++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "test-gstama-polyacleanup": { + "content": [ + [ + "polya_num\tpolya_num_count", + "0\t11", + "1\t1" + ], + [ + "GGAAGCACTTTTTTCCTGTATAGCAAAATGAGTTCAAGATATTCTTTGCCTAATTTCAGCTCTAGCTAGAACCAGTCAATATGGAAATAAACAATGAGGGTATCTAACCTACTGAACACTGAACCATCAGCCTAACTCTATGCAATATAGTCATACTAAAATATTTCTCATAAAAAAGTTCTTAACAGTTCGTTCACTATATCTTTCACGCAGTTATTTTATAGAATAAGCAAAGTAGGGCATGTGAAACACTTTAGCTTAGCTTCTAGCATCCAGTAGCGGTGCTCAAAAATGTTAGATCATTTATGTAACAATCTGCTAGGTTATAACATTCAGTGAGCCTTGGTACTTTTCATTGAACAGCTGGTATAGAGGCTAGGGATAGGGAGCTGCAGTTCATTTTCCATGCCCCTACCCGAGTTCTCTTGGCTAAATGTGATACGCATTTAAGGCCCAGAACCTGCTGTTTAAAAGGTTGTGGTAAACTATTTTGTATACCAAAGACTTCTCTGTAATAAAGTATGTAAGTACACATGAACATTTTATATGCACGCACATTTTAAATCATCTGCACATTGAGATTCTACACTTTTCTCAAGGGCACATCTCTATTCCGTTTCTTTGTAAATTTGACTTCTACCTAACAATATGCAATTGCTGGGATTTTTTTCCCTAACAGTATGAAAGTTGTCTTTAAATAGTAAAAGCACCACAATCTATTAACACCACATGTTATCTTTAAACTGAAATATTTTAGTGATGTCTTGGACATCAAAATAATTTCTTAAGGTGGACTCTTGAGTATGTGGGTCCAGCCCAGGTCTGCAGTTTGTGCAGACATAGAAAAAAGAGGAACTTTAAATATTCAGAAAAAGTTAACAGGCTAGCTTTAAAATACTGCTGGAAATTAAATTTCTTCAGAGTTGGCAAGCATGGGCTATTGATCAAAATATGAATTAAACGGATTTACATCATTAAGAAAAAAACAAATCCATGTTATTGTGCTGTGAAATTTCCATGATGCCTTTCAAATAGGCTGCTCACAAATTTTTTTATAATTCTAAATCACTCGCTTTTTGATGGAAAAAAGAATACAGATGGACTGTGTTTTACCTATGTGAAAGTCACCAATCCATTTAAAATAAAATCCAAGAGGGCATATACAGTCTAATCAAGTCATCATTTTCCTGATTAATAAGAACTACACTTTACACAAAATACTTTATCAGCAGCTGTTTTCATCAAAAAATCAGTAGTCAGTTTCACAGTTGAAAAAGTTACACATTAAAATATTTTACAATTCATTATATATTCACCAGGTTCCCATTTTCTAAGGGGCTTTTAATATAAAGCAGAATAGAACACTGTCTCTACTAAAAATACAAAAATTAGCTGGGAGTGGTGGCATGCTCCTATAGTCCTAGCTACTCAGGAGGCTGAGGTGGGAGGATGGCTTGAACCCAGGAGGTCAAGGCTGCAGTGAGCCGAAATTGCACCACTGCATTCCAGGCCGGGCAAAAGAGCCAGACCCTGTCTCAAAAAAAAAAGTTTACATTGTATTTCCTACTCTTAGTTACACTAAGCTAGACAGCAGATGACTAGAGGGTGTGATATATTTACTGAGTGACTCGAAATCCATTTTAAACTTGGAAATGTAAAAACTAACTTCTTTCCACTCATTTTCAGGGTCATTACTGAGAGATAATAAATGACAGAATAAGGAAATAATCACTGTAAATACTTAGGGACCTGAATAAGAGAAAGGAAGGGAAAGTAAAGGGATCTAACATTTATTGGGCACCTTCTGTGTTCCAAGGATTGTGATAGGTTCTTTGCATATCTCATGTAATTTAATTCTCACAATGGCCTTACGAAGCAGGTATTATTCCCATTTTACAGACAAAGAAAATGAGTCTTGAGAGCCTGCATAACGTGTCTAACACTACACAGATGAGAGGCAGTGGAACTTGGTTCCAAATCCTAATCTGCTTGATTCCAAGGACCATGATCTGTATATACACTGGGCTTCTAAACAACTCTGCCCCACTGCAGTGAAAAGAGTCTCAAACACAGACTAGAGTCACACAACTTTTGTGTTTCATCCTTCTTCTCCTGTTTGACAATGTCAGTTAAGTTAATGAGCTTTTCCATTGCCTCGACTTGCCTATTCAGGTGCTTCAAATACATCCCACATGCACGACAATAGGACTCCAAAAGCAGGCCAAACCTCTGGCTAAGTGTTTTATTGTGCATCTCAGATCTAAAAGAATCATGCAAAATTAGAAAAATATATATATAGTCTTAAATCAGTATACAAATAATCTTTGCTAAACAATTTAAACACTCATTTTTGAAATCCAATAAATGTTACAATCATACTAATAATAACATTATTCAAAACCTGTAATTTAGAAGCAAAACCACCATGAGTTTCAGGTAGTTCCTGAATATGTGATTAAATAAACATCTAGTTTTTAGGTTTATTTCAACTAGTTTTCATTGACTAATCTCAGTACAAGATATAAAAGCATGAAAAAAGGAAATTGAGCACAAAAATAATCAAATGAAGAGGGAGGGAACAAAGCGCTCAGTGAATGCTGTTTGACTCTTCTGACACACGTCTACGCTTCTTGTTTTCAACTTAACTTCTGGGTTCCATTTTTAAATTTTAACACTTAAAATATCATATTAGATATAAATCTGTTTCTAAATTTATGAAAAGTTATATGGTTTATGACCTGTAACTTTTGAGTACTGCATATATCACATTCTACAAAACATTTTTTATTCTTAATTAGCTTGTTTTTCAGTAAGAACCACGGGAGTTTGACATTATTGTTCTGAATCTCAAGGTAAAACATTTTTTTTCTTTTTTTGGGGATATTTTAATCCATACACACAGTGAAACCTACAGCAATATTCATCTGGACCTAGAAAATTTTACTTAAGTAGAACAAAAATCTTTAAAAATATTTAAGCTCTCATTCATGACTGAAATTTAGTTTTGAATTTATTACTTTTTAAATTTCAAAGAGCAAAAGTTGAGAAGCTCATCACTGGTACAAAATAGTTTTAGTATGGAAAACTCTTCCAGCCAAACATAAACAAAAGTATATAAGTAATACATATTTATAAATCTATTAAGAAAGCAAGTAATATGTACCTTAAGAATTTAATGGGAAAATAATTAGACTTACTTTAAATGCCAAAAGAAAAAGTGCCCAATCCTTTGATTAGTCAATGCTTTCTTCAGTAAAAATCTCACAAGCAAGTTATCCAAATATTGTTCATATTTTAGGACCTAGGTGATTCAAAAAAAACAAATCAGGTTCAGTTTCTGCATGGCCGATCTAAAGAAAATTTTTTCAGAAAGAAAGTGGATATTACTG", + ">ENST00000472972", + "AACCTACTGAACACTGAACCATCAGCCTAACTCTATGCAATATAGTCATACTAAAATATTTCTCATAAAAAAGTTCTTAACAGTTCGTTCACTATATCTTTCACGCAGTTATTTTATAGAATAAGCAAAGTAGGGCATGTGAAACACTTTAGCTTAGCTTCTAGCATCCAGTAGCGGTGCTCAAAAATGTTAGATCATTTATGTAACAATCTGCTAGGTTATAACATTCAGTGAGCCTTGGTACTTTTCATTGAACAGCTGGTATAGAGGCTAGGGATAGGGAGCTGCAGTTCATTTTCCATGCCCC", + ">ENST00000359963 CDS=261-1934", + "TTTCTTTAAATAAAAACATGAAGGAACATAAAATTTCTTTTCATGCGCTTAGTTCCTTTCCAGTTCTCGACTTTTTTTGTTTTTTTTTTTTGAGAGACGGAGTCTTGCTCTGTTGCCCAGGCTGGTGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGTTCAAGCGATTTTCCTGCCTCAGCCTCCTGAATAGCTGGGACTACAGGTGCGCGCCACCACGCCCAGCTATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATATTGACCAGGCTGGTCTCGAACTCCTGACCTCATGATCCTCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGAGAGCCACTGTGCCCAGCCAGTTCTTGACCTTTTCATTTTGTGTTTCTATCAGATGCTCTTCCTTTCCTATGATAAGAGCAGGATTCAATTCTATTAAGATTTTTAAACTGAGTACCTATGTGGGCTTTGGGCGTGCAAAACACAGTGCAGCAATCTCTTCCCAACTATTTGAGCATTCCCTGCATGATATTCTGACATATATGGACTTATGTCTAGATGTCACTTTAGGAGTCTGAAAACATCAGTTGCAGCTTACAAGAGTGGTCAGTCCTTCCTGTTGTGGTTATTTGAAAAAAAAGAAGGGACTATCATCTTAAAGCACAGAGAGAGAGAGAGAGCAGGAGAAAGAGCTGCTGTGGTGGCAGGCAGAAATGTAACTTAAAAAGAAAAAAATCCTTGCCTGGCAAAGTGGCTCATGCCTATAATTCCTGCACTTTGGGAGGCTGAGACAGGAAGATCGCTTGAGTCCAGGAGTTCAAGACTAGCCTGGACAACATAGTGAGACCCTATCTCTACAAAAATAAAAATTAAAAAAAATTAGCCAGGCATGGGCCGGGCATGGTGGCTCAAGCCTTTAATCCCAGCACTTTGGGAGCCCAAGGTGGGTGGATCAGCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACGTGGAGAAACCCCATCTCTACTAAAAATACAAAACAGTAGCCGGATGTGATGGCACATGCCTGTAATCCCAGCTATTTGAGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCAGAGGTTGTGGTGAGCTGAGATGACACTATTGTACCCCAGCCTGGGCAACAAGAGCAAAACTCTGCCTCAAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGTGATGCATACCTGTAGTCCCAGCTACTCAGGAGGCTGAGTGGGGGGATCACTTAAGCCCAGGAGATCGAGGTTGCAGTGAGCTGTGATTGTGCCACTGCACTCCAGCCTAAGAGACAGAGCAAGACCCTGTCTCAACAAAACAAAACAAAACCAGCAAACATCCTTGGCATAGATAACAGAAGATAAGAACACATACTTTAGGACTATACTAAGGTTGCTGTGTAGGTGAGGAGAAAGCTGAGGGTAGGGGGAAGGGCTAGGATTGGACAACCTTGGGCATTAAAGAAGGGGTTTGAGCAGAGCTGAGTGGGTTTGGCACCTAATACGCAAAGCTTTTTCCACTTTTTTAACTTCCAAGTTACTCTAGGAAAAATCAGAACCTATGGGACAGAATCTAGGAGATGAGAAGGTACAATCTTTTAGAATCATAAAAATAAAAAAGCTTTAGGCATATGCAGAGAGAATGAGACTCAAGAAACCATTGTCTTATAGCACGCATATTAGCCGCAACACAGCAAAACAAAATTTTATTTATTTATTTATTTATTTTGAGACAGAGTCTTGCTCTGTCACCCAGGCATAGTGACTGGTGTGGCCCAGGCACCAGTGCAGCAGTGCAGTCTCAGCTCACTGCAACCTCTGCCTCCTGGGCTCAAATGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTCCACCACCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCGCCATGTTGGTCAGGGTGGTCTCAAACTTTGGACCTCAGGTGATCCACCTGCCTCGGCCTCCCCAAATGCTGAGATTACAG" + ], + [ + "", + ">tail_ENST00000472972", + "", + ">tail_ENST00000359963 CDS=261-1934", + "" + ], + [ + "versions.yml:md5,dff6214a93a250748705dbd8ec455fec" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:44:18.309783" + } +} \ No newline at end of file diff --git a/modules/nf-core/gstama/polyacleanup/tests/nextflow.config b/modules/nf-core/gstama/polyacleanup/tests/nextflow.config new file mode 100644 index 00000000000..0ffcbb55a35 --- /dev/null +++ b/modules/nf-core/gstama/polyacleanup/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.prefix = { "${meta.id}_tama" } +} diff --git a/modules/nf-core/happy/sompy/main.nf b/modules/nf-core/happy/sompy/main.nf index e0c34e262de..ba23fd16765 100644 --- a/modules/nf-core/happy/sompy/main.nf +++ b/modules/nf-core/happy/sompy/main.nf @@ -54,7 +54,7 @@ process HAPPY_SOMPY { """ stub: - def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}.features.csv diff --git a/modules/nf-core/happy/sompy/meta.yml b/modules/nf-core/happy/sompy/meta.yml index 3dd2b911be8..8a04a601739 100644 --- a/modules/nf-core/happy/sompy/meta.yml +++ b/modules/nf-core/happy/sompy/meta.yml @@ -13,8 +13,7 @@ tools: homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html" documentation: "https://github.com/Illumina/hap.py/blob/master/doc/sompy.md" tool_dev_url: "https://github.com/Illumina/hap.py" - - licence: "['BSD-2-clause']" + licence: ["BSD-2-clause"] input: - meta: @@ -22,6 +21,31 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + - meta2: + type: map + description: | + Groovy Map containing fasta file information + e.g. [ id:'test2'] + - meta3: + type: map + description: | + Groovy Map containing fai file information + e.g. [ id:'test3'] + - meta4: + type: map + description: | + Groovy Map containing false_positives_bed file information + e.g. [ id:'test4'] + - meta5: + type: map + description: | + Groovy Map containing ambiguous_beds file information + e.g. [ id:'test5'] + - meta6: + type: map + description: | + Groovy Map containing bam file information + e.g. [ id:'test6'] - query_vcf: type: file description: VCF/GVCF file to query diff --git a/modules/nf-core/happy/sompy/tests/main.nf.test b/modules/nf-core/happy/sompy/tests/main.nf.test new file mode 100644 index 00000000000..f4919c73f7b --- /dev/null +++ b/modules/nf-core/happy/sompy/tests/main.nf.test @@ -0,0 +1,127 @@ +nextflow_process { + + name "Test Process HAPPY_SOMPY" + script "../main.nf" + process "HAPPY_SOMPY" + + tag "modules" + tag "modules_nfcore" + tag "happy" + tag "happy/sompy" + + test("homo_sapiens - vcf") { + config './nextflow.config' + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'test2' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'test3' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [[],[]] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.stats, + process.out.versions, + file(process.out.metrics[0][1]).name, + file(process.out.features[0][1]).name).match()} + ) + } + + } + test("homo_sapiens - vcf - bam") { + config './nextflow.config' + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'test2' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'test3' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [[],[]] + input[4] = [[],[]] + input[5] = [[ id:'test2' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.stats, + process.out.versions, + file(process.out.metrics[0][1]).name, + file(process.out.features[0][1]).name).match()} + ) + } + + } + test("homo_sapiens - vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'test2' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'test3' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [[],[]] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/happy/sompy/tests/main.nf.test.snap b/modules/nf-core/happy/sompy/tests/main.nf.test.snap new file mode 100644 index 00000000000..b6b25e6decf --- /dev/null +++ b/modules/nf-core/happy/sompy/tests/main.nf.test.snap @@ -0,0 +1,111 @@ +{ + "homo_sapiens - vcf": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.stats.csv:md5,8b35dd00bf7b5bd697a05d73fb8c0816" + ] + ], + [ + "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc" + ], + "test.metrics.json", + "test.features.csv" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T08:56:57.589412212" + }, + "homo_sapiens - vcf - bam": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.stats.csv:md5,5e9aae3e92641f1934c10fe88f250e59" + ] + ], + [ + "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc" + ], + "test.metrics.json", + "test.features.csv" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T08:57:13.752402851" + }, + "homo_sapiens - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.features.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.metrics.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc" + ], + "features": [ + [ + { + "id": "test" + }, + "test.features.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "id": "test" + }, + "test.metrics.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test" + }, + "test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T14:39:09.160343644" + } +} \ No newline at end of file diff --git a/modules/nf-core/happy/sompy/tests/nextflow.config b/modules/nf-core/happy/sompy/tests/nextflow.config new file mode 100644 index 00000000000..3a95dc4e6f3 --- /dev/null +++ b/modules/nf-core/happy/sompy/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: HAPPY_SOMPY { + ext.args = '--feature-table hcc.mutect.snv' + } +} diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test new file mode 100644 index 00000000000..fd132089a41 --- /dev/null +++ b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test @@ -0,0 +1,40 @@ + +nextflow_process { + + name "Test Process PICARD_BEDTOINTERVALLIST" + script "../main.nf" + process "PICARD_BEDTOINTERVALLIST" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/bedtointervallist" + + test("test-picard-bedtointervallist") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + input[1] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] + input[2] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap new file mode 100644 index 00000000000..6abbf0e92f9 --- /dev/null +++ b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test-picard-bedtointervallist": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c" + ] + ], + "1": [ + "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65" + ], + "interval_list": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c" + ] + ], + "versions": [ + "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:39:08.82372" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/cleansam/meta.yml b/modules/nf-core/picard/cleansam/meta.yml index ae98e2d2249..a74fe2e100d 100644 --- a/modules/nf-core/picard/cleansam/meta.yml +++ b/modules/nf-core/picard/cleansam/meta.yml @@ -21,7 +21,7 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - sam: + - bam: type: file description: BAM file pattern: "*.{bam}" @@ -35,7 +35,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - - sam: + - bam: type: file description: Cleaned BAM file pattern: "*.{bam}" diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test b/modules/nf-core/picard/cleansam/tests/main.nf.test new file mode 100644 index 00000000000..5d80739a472 --- /dev/null +++ b/modules/nf-core/picard/cleansam/tests/main.nf.test @@ -0,0 +1,40 @@ + +nextflow_process { + + name "Test Process PICARD_CLEANSAM" + script "../main.nf" + process "PICARD_CLEANSAM" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/cleansam" + + test("test-picard-cleansam") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test.snap b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap new file mode 100644 index 00000000000..63e2927e57a --- /dev/null +++ b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-picard-cleansam": { + "content": [ + "798439cbd7fd81cbcc5078022dc5479d", + [ + "versions.yml:md5,f99b648dc3d150a0561094e3a142ee22" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:36:05.525364" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/picard/cleansam/nextflow.config b/modules/nf-core/picard/cleansam/tests/nextflow.config similarity index 50% rename from tests/modules/nf-core/picard/cleansam/nextflow.config rename to modules/nf-core/picard/cleansam/tests/nextflow.config index 7fbfaaa64f0..06a6daceb45 100644 --- a/tests/modules/nf-core/picard/cleansam/nextflow.config +++ b/modules/nf-core/picard/cleansam/tests/nextflow.config @@ -1,7 +1,4 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'PICARD_CLEANSAM'{ ext.prefix = { "${meta.id}.cleaned"} } diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test new file mode 100644 index 00000000000..5b67774f720 --- /dev/null +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test @@ -0,0 +1,112 @@ + +nextflow_process { + + name "Test Process PICARD_COLLECTMULTIPLEMETRICS" + script "../main.nf" + process "PICARD_COLLECTMULTIPLEMETRICS" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/collectmultiplemetrics" + + test("test-picard-collectmultiplemetrics") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[id:'genome'],[]] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.metrics[0][1].collect { file(it).name }.toSorted(), + process.out.pdf[0][1].collect { file(it).name }.toSorted(), + process.out.versions + ).match() + } + ) + } + } + + test("test-picard-collectmultiplemetrics-nofasta") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [[id:'genome'],[]] + input[2] = [[id:'genome'],[]] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.metrics[0][1].collect { file(it).name }.toSorted(), + process.out.pdf[0][1].collect { file(it).name }.toSorted(), + process.out.versions + ).match() + } + ) + } + } + + test("test-picard-collectmultiplemetrics-cram") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.metrics[0][1].collect { file(it).name }.toSorted(), + process.out.pdf[0][1].collect { file(it).name }.toSorted(), + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap new file mode 100644 index 00000000000..1859541b6dd --- /dev/null +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap @@ -0,0 +1,80 @@ +{ + "test-picard-collectmultiplemetrics": { + "content": [ + [ + "test.CollectMultipleMetrics.alignment_summary_metrics", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "test.CollectMultipleMetrics.insert_size_metrics", + "test.CollectMultipleMetrics.quality_by_cycle_metrics", + "test.CollectMultipleMetrics.quality_distribution_metrics" + ], + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "test.CollectMultipleMetrics.insert_size_histogram.pdf", + "test.CollectMultipleMetrics.quality_by_cycle.pdf", + "test.CollectMultipleMetrics.quality_distribution.pdf", + "test.CollectMultipleMetrics.read_length_histogram.pdf" + ], + [ + "versions.yml:md5,b68b83e8dd0f9360453213acad639338" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:03:36.631174" + }, + "test-picard-collectmultiplemetrics-cram": { + "content": [ + [ + "test.CollectMultipleMetrics.alignment_summary_metrics", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "test.CollectMultipleMetrics.insert_size_metrics", + "test.CollectMultipleMetrics.quality_by_cycle_metrics", + "test.CollectMultipleMetrics.quality_distribution_metrics" + ], + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "test.CollectMultipleMetrics.insert_size_histogram.pdf", + "test.CollectMultipleMetrics.quality_by_cycle.pdf", + "test.CollectMultipleMetrics.quality_distribution.pdf", + "test.CollectMultipleMetrics.read_length_histogram.pdf" + ], + [ + "versions.yml:md5,b68b83e8dd0f9360453213acad639338" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:04:13.955902" + }, + "test-picard-collectmultiplemetrics-nofasta": { + "content": [ + [ + "test.CollectMultipleMetrics.alignment_summary_metrics", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "test.CollectMultipleMetrics.insert_size_metrics", + "test.CollectMultipleMetrics.quality_by_cycle_metrics", + "test.CollectMultipleMetrics.quality_distribution_metrics" + ], + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "test.CollectMultipleMetrics.insert_size_histogram.pdf", + "test.CollectMultipleMetrics.quality_by_cycle.pdf", + "test.CollectMultipleMetrics.quality_distribution.pdf", + "test.CollectMultipleMetrics.read_length_histogram.pdf" + ], + [ + "versions.yml:md5,b68b83e8dd0f9360453213acad639338" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:03:54.707587" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/fastqtosam/tests/main.nf.test b/modules/nf-core/picard/fastqtosam/tests/main.nf.test new file mode 100644 index 00000000000..ad3d52374a0 --- /dev/null +++ b/modules/nf-core/picard/fastqtosam/tests/main.nf.test @@ -0,0 +1,100 @@ + +nextflow_process { + + name "Test Process PICARD_FASTQTOSAM" + script "../main.nf" + process "PICARD_FASTQTOSAM" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/fastqtosam" + + test("test-picard-fastqtosam-single") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + + test("test-picard-fastqtosam-paired") { + + when { + process { + """ + input[0] = [ + [ 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) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + + test("test-picard-fastqtosam-paired-custom-samplename") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ 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) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap new file mode 100644 index 00000000000..2f999dcc9c9 --- /dev/null +++ b/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap @@ -0,0 +1,41 @@ +{ + "test-picard-fastqtosam-paired-custom-samplename": { + "content": [ + "e3cfa46b13cc4fc425cccae944f43b10", + [ + "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T09:50:01.762254" + }, + "test-picard-fastqtosam-single": { + "content": [ + "e6a4aa204d980e177a0458596f0a70ac", + [ + "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T09:49:32.460549" + }, + "test-picard-fastqtosam-paired": { + "content": [ + "e3cfa46b13cc4fc425cccae944f43b10", + [ + "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T09:49:47.018269" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/fastqtosam/tests/nextflow.config b/modules/nf-core/picard/fastqtosam/tests/nextflow.config new file mode 100644 index 00000000000..22294c05eb3 --- /dev/null +++ b/modules/nf-core/picard/fastqtosam/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'PICARD_FASTQTOSAM' { + ext.args = "--SAMPLE_NAME CustomSample" + } +} diff --git a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test new file mode 100644 index 00000000000..b45bdde582d --- /dev/null +++ b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test @@ -0,0 +1,40 @@ + +nextflow_process { + + name "Test Process PICARD_FIXMATEINFORMATION" + script "../main.nf" + process "PICARD_FIXMATEINFORMATION" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/fixmateinformation" + + test("test-picard-fixmateinformation") { + + 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) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap new file mode 100644 index 00000000000..799173a6f92 --- /dev/null +++ b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-picard-fixmateinformation": { + "content": [ + "ddd0dc8f0cf1996d19dae51681187114", + [ + "versions.yml:md5,36a59533c3e8578b046c4c2ec9caa8d4" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T09:45:26.092108" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/fixmateinformation/tests/nextflow.config b/modules/nf-core/picard/fixmateinformation/tests/nextflow.config new file mode 100644 index 00000000000..c6b0432e8a7 --- /dev/null +++ b/modules/nf-core/picard/fixmateinformation/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: PICARD_FIXMATEINFORMATION { + ext.prefix = { "${meta.id}.fixed" } + } +} diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index e47b74f787e..a4b27c88e5f 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -50,8 +50,8 @@ process PICARD_LIFTOVERVCF { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.lifted.vcf.gz - touch ${prefix}.unlifted.vcf.gz + echo | gzip > ${prefix}.lifted.vcf.gz + echo | gzip > ${prefix}.unlifted.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test b/modules/nf-core/picard/liftovervcf/tests/main.nf.test new file mode 100644 index 00000000000..7b42102dec5 --- /dev/null +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test @@ -0,0 +1,84 @@ + +nextflow_process { + + name "Test Process PICARD_LIFTOVERVCF" + script "../main.nf" + process "PICARD_LIFTOVERVCF" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/liftovervcf" + + test("test-picard-liftovervcf") { + + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf_lifted[0][1]).vcf.summary, + path(process.out.vcf_unlifted[0][1]).vcf.variantsMD5, + process.out.versions + ).match() + } + ) + } + } + + test("test-picard-liftovervcf-stubs") { + options '-stub' + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.vcf_lifted[0][1]).name, + file(process.out.vcf_unlifted[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap new file mode 100644 index 00000000000..585ea369e8b --- /dev/null +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap @@ -0,0 +1,30 @@ +{ + "test-picard-liftovervcf-stubs": { + "content": [ + "test.lifted.vcf.gz", + "test.unlifted.vcf.gz", + [ + "versions.yml:md5,e1aaacb3c05a0d822f7abdcf3a55fa91" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T09:38:05.840798" + }, + "test-picard-liftovervcf": { + "content": [ + "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]", + "39a9de5185d94289283bd27cfcdeba97", + [ + "versions.yml:md5,e1aaacb3c05a0d822f7abdcf3a55fa91" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T09:41:33.022998" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/liftovervcf/tests/nextflow.config b/modules/nf-core/picard/liftovervcf/tests/nextflow.config new file mode 100644 index 00000000000..d89d78651b9 --- /dev/null +++ b/modules/nf-core/picard/liftovervcf/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = "--WARN_ON_MISSING_CONTIG true" +} diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test new file mode 100644 index 00000000000..f755447ff4c --- /dev/null +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test @@ -0,0 +1,38 @@ + +nextflow_process { + + name "Test Process PICARD_RENAMESAMPLEINVCF" + script "../main.nf" + process "PICARD_RENAMESAMPLEINVCF" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/renamesampleinvcf" + + test("test-picard-renamesampleinvcf") { + + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', 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/picard/renamesampleinvcf/tests/main.nf.test.snap b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap new file mode 100644 index 00000000000..a9bf7b7bf04 --- /dev/null +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-picard-renamesampleinvcf": { + "content": [ + "e21a2349f41663d1fc38f47fbe65a6d5", + [ + "versions.yml:md5,d4de734264e0c3b33d23e4a40de26a5f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T09:32:02.18878" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/sortsam/tests/main.nf.test b/modules/nf-core/picard/sortsam/tests/main.nf.test new file mode 100644 index 00000000000..9d9af09ea77 --- /dev/null +++ b/modules/nf-core/picard/sortsam/tests/main.nf.test @@ -0,0 +1,40 @@ + +nextflow_process { + + name "Test Process PICARD_SORTSAM" + script "../main.nf" + process "PICARD_SORTSAM" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/sortsam" + + test("test-picard-sortsam") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) + ] + input[1] = "queryname" + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/picard/sortsam/tests/main.nf.test.snap b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap new file mode 100644 index 00000000000..bf447b8d135 --- /dev/null +++ b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-picard-sortsam": { + "content": [ + "b9847fed94d2b7286e18caaa099658ce", + [ + "versions.yml:md5,f53876b7c58b5aa1564606f3c9c34108" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T09:23:48.485054" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/sortsam/tests/nextflow.config b/modules/nf-core/picard/sortsam/tests/nextflow.config new file mode 100644 index 00000000000..8512101e96f --- /dev/null +++ b/modules/nf-core/picard/sortsam/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: PICARD_SORTSAM { + ext.prefix = { "${meta.id}.sorted" } + } +} diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test b/modules/nf-core/picard/sortvcf/tests/main.nf.test new file mode 100644 index 00000000000..9df73ad430f --- /dev/null +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test @@ -0,0 +1,44 @@ + +nextflow_process { + + name "Test Process PICARD_SORTVCF" + script "../main.nf" + process "PICARD_SORTVCF" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/sortvcf" + + test("test-picard-sortvcf") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).linesGzip[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap new file mode 100644 index 00000000000..db80323bfe5 --- /dev/null +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "test-picard-sortvcf": { + "content": [ + [ + "##FILTER=", + "##FORMAT=", + "##FORMAT=", + "##INFO=", + "##INFO=" + ], + [ + "versions.yml:md5,11949a1af95080dcc5bd1c75d68dee71" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T09:20:13.124551" + } +} \ No newline at end of file diff --git a/modules/nf-core/untarfiles/environment.yml b/modules/nf-core/untarfiles/environment.yml index e479f80d548..be5a6da9d88 100644 --- a/modules/nf-core/untarfiles/environment.yml +++ b/modules/nf-core/untarfiles/environment.yml @@ -1,9 +1,11 @@ name: untarfiles + channels: - conda-forge - bioconda - defaults + dependencies: - - conda-forge::sed=4.7 - bioconda::grep=3.4 + - conda-forge::sed=4.7 - conda-forge::tar=1.34 diff --git a/modules/nf-core/wittyer/Dockerfile b/modules/nf-core/wittyer/Dockerfile index 3955699c92d..fae697ab9dc 100644 --- a/modules/nf-core/wittyer/Dockerfile +++ b/modules/nf-core/wittyer/Dockerfile @@ -1,11 +1,11 @@ -FROM mcr.microsoft.com/dotnet/sdk:6.0 as builder +FROM mcr.microsoft.com/dotnet/sdk:6.0@sha256:6df1177e48b55272316d08f19cb383483af82aca5cdc67a76c414bc200847624 as builder WORKDIR /src COPY . /src RUN cd Wittyer \ && dotnet publish -f net6.0 -r linux-x64 -c Release -o /output \ && chmod +x /output/Wittyer -FROM mcr.microsoft.com/dotnet/runtime:6.0 +FROM mcr.microsoft.com/dotnet/runtime:6.0@sha256:437cda84bdce26ce074d88b63abeec567c7226d73e8b911605077468e1d5c8d5 LABEL git_repository=https://git.illumina.com/DASTE/Ilmn.Das.App.Wittyer.git WORKDIR /opt/Wittyer RUN apt-get -y update && apt-get -y install tabix libunwind8 openssl procps diff --git a/subworkflows/nf-core/bcl_demultiplex/main.nf b/subworkflows/nf-core/bcl_demultiplex/main.nf index 3816f310f9c..129b2f1b554 100644 --- a/subworkflows/nf-core/bcl_demultiplex/main.nf +++ b/subworkflows/nf-core/bcl_demultiplex/main.nf @@ -64,65 +64,67 @@ workflow BCL_DEMULTIPLEX { } // Generate meta for each fastq - ch_fastq_with_meta = ch_fastq - // reshapes the channel from a single emit of [meta, [fastq, fastq, fastq...]] - // to emits per fastq file like [meta, fastq] - .transpose() - .map { fc_meta, fastq -> - def meta = [:] - meta.id = fastq.getSimpleName().toString() - ~/_R[0-9]_001.*$/ - meta.samplename = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/ - meta.fcid = fc_meta.id - meta.lane = fc_meta.lane - // The buffered input stream allows reading directly from cloud storage - // It will not make a local copy of the file. - fastq.withInputStream { - InputStream gzipStream = new java.util.zip.GZIPInputStream(it) - Reader decoder = new InputStreamReader(gzipStream, 'ASCII') - BufferedReader buffered = new BufferedReader(decoder) - line = buffered.readLine() - buffered.close() - } - if ( line != null && line.startsWith('@') ) { - line = line.substring(1) - // expected format is like: - // xx:yy:FLOWCELLID:LANE:... (seven fields) - fields = line.split(':') - // CASAVA 1.8+ format, from https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/FileFormat_FASTQ-files_swBS.htm - // "@::::::: :::" - sequencer_serial = fields[0] - run_nubmer = fields[1] - fcid = fields[2] - lane = fields[3] - index = fields[-1] =~ /[GATC+-]/ ? fields[-1] : "" - ID = [fcid, lane].join(".") - PU = [fcid, lane, index].findAll().join(".") - PL = "ILLUMINA" - SM = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/ - meta.readgroup = [ - "ID": ID, - "SM": SM, - "PL": PL, - "PU": PU - ] - meta.empty = false - } else { - println "No reads were found in FASTQ file: ${fastq}" - meta.readgroup = [:] - meta.empty = true - } - return [meta, fastq] + ch_fastq + // reshapes the channel from a single emit of [meta, [fastq, fastq, fastq...]] + // to emits per fastq file like [meta, fastq] + .transpose() + .map { fc_meta, fastq -> + def meta = [:] + meta.id = fastq.getSimpleName().toString() - ~/_R[0-9]_001.*$/ + meta.samplename = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/ + meta.fcid = fc_meta.id + meta.lane = fc_meta.lane + // The buffered input stream allows reading directly from cloud storage + // It will not make a local copy of the file. + def line = "" + fastq.withInputStream { fq -> + def gzipStream = new java.util.zip.GZIPInputStream(fq) + def decoder = new InputStreamReader(gzipStream, 'ASCII') + def buffered = new BufferedReader(decoder) + line = buffered.readLine() + buffered.close() } - // Group by the meta id so that we can find mate pairs if they exist - .groupTuple(by: [0]) - .map { meta, fastq -> - meta.single_end = fastq.size() == 1 - return [meta, fastq.flatten()] - } - .branch { - fastq : it[0].empty == false - empty_fastq : it[0].empty == true + if ( line != null && line.startsWith('@') ) { + line = line.substring(1) + // expected format is like: + // xx:yy:FLOWCELLID:LANE:... (seven fields) + fields = line.split(':') + // CASAVA 1.8+ format, from https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/FileFormat_FASTQ-files_swBS.htm + // "@::::::: :::" + sequencer_serial = fields[0] + run_nubmer = fields[1] + fcid = fields[2] + lane = fields[3] + index = fields[-1] =~ /[GATC+-]/ ? fields[-1] : "" + ID = [fcid, lane].join(".") + PU = [fcid, lane, index].findAll().join(".") + PL = "ILLUMINA" + SM = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/ + meta.readgroup = [ + "ID": ID, + "SM": SM, + "PL": PL, + "PU": PU + ] + meta.empty = false + } else { + println "No reads were found in FASTQ file: ${fastq}" + meta.readgroup = [:] + meta.empty = true } + return [meta, fastq] + } + // Group by the meta id so that we can find mate pairs if they exist + .groupTuple(by: [0]) + .map { meta, fastq -> + meta.single_end = fastq.size() == 1 + return [meta, fastq.flatten()] + } + .branch { + fastq : it[0].empty == false + empty_fastq : it[0].empty == true + } + .set{ch_fastq_with_meta} emit: fastq = ch_fastq_with_meta.fastq diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index e770d91b974..b54fc16c71a 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,10 +2,6 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) { def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') def filename = "params_${timestamp}.json" def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) @@ -102,14 +98,16 @@ def checkCondaChannels() { // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda'] + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + + required_channels_in_order.eachWithIndex { channel, index -> + if (index < required_channels_in_order.size() - 1) { + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + } } if (channels_missing | channel_priority_violation) { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926bf6dd..a09572e5bbf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c39278..cbd8495bb60 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,9 +2,6 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE { // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + @@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) { // def workflowCitation() { def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") + def manifest_doi = workflow.manifest.doi.tokenize(",") // Using a loop to handle multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + manifest_doi.each { doi_ref -> + temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + } return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + @@ -84,7 +83,7 @@ def workflowCitation() { // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +101,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } return yaml.dumpAsMap(versions).trim() } @@ -124,7 +123,7 @@ def workflowVersionToYAML() { def softwareVersionsToYAML(ch_versions) { return ch_versions .unique() - .map { processVersionsFromYAML(it) } + .map { version -> processVersionsFromYAML(version) } .unique() .mix(Channel.of(workflowVersionToYAML())) } @@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { + summary_params.keySet().each { group -> def group_params = summary_params.get(group) // This gets the parameters of that particular group if (group_params) { summary_section += "

$group

\n" summary_section += "
\n" - for (param in group_params.keySet()) { + group_params.keySet().sort().each { param -> summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" } summary_section += "
\n" } } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" @@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) { // nf-core logo // def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map String.format( """\n ${dashedLine(monochrome_logs)} @@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) { // Return dashed line // def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map return "-${colors.dim}----------------------------------------------------${colors.reset}-" } @@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) { // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi } def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } @@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } @@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); output_tf.delete() } @@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" @@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 00000000000..4994303ea0b --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 00000000000..f7d9f028850 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 00000000000..842dc432af7 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 00000000000..0907ac58f00 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json new file mode 100644 index 00000000000..331e0d2f443 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "$defs": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/input_output_options" + }, + { + "$ref": "#/$defs/generic_options" + } + ] +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index e6efda55068..19e00530590 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -34,69 +34,21 @@ bamtools/convert: bamtools/split: - modules/nf-core/bamtools/split/** - tests/modules/nf-core/bamtools/split/** -bandage/image: - - modules/nf-core/bandage/image/** - - tests/modules/nf-core/bandage/image/** basicpy: - modules/nf-core/basicpy/** - tests/modules/nf-core/basicpy/** bbmap/align: - modules/nf-core/bbmap/align/** - tests/modules/nf-core/bbmap/align/** -bbmap/bbnorm: - - modules/nf-core/bbmap/bbnorm/** - - tests/modules/nf-core/bbmap/bbnorm/** -bbmap/index: - - modules/nf-core/bbmap/index/** - - tests/modules/nf-core/bbmap/index/** -bbmap/pileup: - - modules/nf-core/bbmap/pileup/** - - tests/modules/nf-core/bbmap/pileup/** 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/** -bcftools/roh: - - modules/nf-core/bcftools/roh/** - - tests/modules/nf-core/bcftools/roh/** -bcftools/split: - - modules/nf-core/bcftools/split/** - - tests/modules/nf-core/bcftools/split/** -beagle5/beagle: - - modules/nf-core/beagle5/beagle/** - - tests/modules/nf-core/beagle5/beagle/** -bedtools/groupby: - - modules/nf-core/bedtools/groupby/** - - tests/modules/nf-core/bedtools/groupby/** bedtools/intersect: - modules/nf-core/bedtools/intersect/** - tests/modules/nf-core/bedtools/intersect/** -bedtools/jaccard: - - modules/nf-core/bedtools/jaccard/** - - tests/modules/nf-core/bedtools/jaccard/** -bedtools/makewindows: - - modules/nf-core/bedtools/makewindows/** - - tests/modules/nf-core/bedtools/makewindows/** -bedtools/maskfasta: - - modules/nf-core/bedtools/maskfasta/** - - tests/modules/nf-core/bedtools/maskfasta/** -bedtools/multiinter: - - modules/nf-core/bedtools/multiinter/** - - tests/modules/nf-core/bedtools/multiinter/** -bedtools/shift: - - modules/nf-core/bedtools/shift/** - - tests/modules/nf-core/bedtools/shift/** -bedtools/slop: - - modules/nf-core/bedtools/slop/** - - tests/modules/nf-core/bedtools/slop/** -bedtools/split: - - modules/nf-core/bedtools/split/** - - tests/modules/nf-core/bedtools/split/** -bedtools/subtract: - - modules/nf-core/bedtools/subtract/** - - tests/modules/nf-core/bedtools/subtract/** bedtools/unionbedg: - modules/nf-core/bedtools/unionbedg/** - tests/modules/nf-core/bedtools/unionbedg/** @@ -407,27 +359,9 @@ gappa/examineheattree: gatk/indelrealigner: - modules/nf-core/gatk/indelrealigner/** - tests/modules/nf-core/gatk/indelrealigner/** -gatk/unifiedgenotyper: - - modules/nf-core/gatk/unifiedgenotyper/** - - tests/modules/nf-core/gatk/unifiedgenotyper/** -gatk4/calibratedragstrmodel: - - modules/nf-core/gatk4/calibratedragstrmodel/** - - tests/modules/nf-core/gatk4/calibratedragstrmodel/** gatk4/cnnscorevariants: - modules/nf-core/gatk4/cnnscorevariants/** - tests/modules/nf-core/gatk4/cnnscorevariants/** -gatk4/collectreadcounts: - - modules/nf-core/gatk4/collectreadcounts/** - - tests/modules/nf-core/gatk4/collectreadcounts/** -gatk4/collectsvevidence: - - modules/nf-core/gatk4/collectsvevidence/** - - tests/modules/nf-core/gatk4/collectsvevidence/** -gatk4/composestrtablefile: - - modules/nf-core/gatk4/composestrtablefile/** - - tests/modules/nf-core/gatk4/composestrtablefile/** -gatk4/condensedepthevidence: - - modules/nf-core/gatk4/condensedepthevidence/** - - tests/modules/nf-core/gatk4/condensedepthevidence/** gatk4/createreadcountpanelofnormals: - modules/nf-core/gatk4/createreadcountpanelofnormals/** - tests/modules/nf-core/gatk4/createreadcountpanelofnormals/** @@ -437,21 +371,9 @@ gatk4/createsomaticpanelofnormals: gatk4/determinegermlinecontigploidy: - modules/nf-core/gatk4/determinegermlinecontigploidy/** - tests/modules/nf-core/gatk4/determinegermlinecontigploidy/** -gatk4/fastqtosam: - - modules/nf-core/gatk4/fastqtosam/** - - tests/modules/nf-core/gatk4/fastqtosam/** -gatk4/filterintervals: - - modules/nf-core/gatk4/filterintervals/** - - tests/modules/nf-core/gatk4/filterintervals/** gatk4/filtervarianttranches: - modules/nf-core/gatk4/filtervarianttranches/** - tests/modules/nf-core/gatk4/filtervarianttranches/** -gatk4/gatherbqsrreports: - - modules/nf-core/gatk4/gatherbqsrreports/** - - tests/modules/nf-core/gatk4/gatherbqsrreports/** -gatk4/gatherpileupsummaries: - - modules/nf-core/gatk4/gatherpileupsummaries/** - - tests/modules/nf-core/gatk4/gatherpileupsummaries/** gatk4/genotypegvcfs: - modules/nf-core/gatk4/genotypegvcfs/** - tests/modules/nf-core/gatk4/genotypegvcfs/** @@ -461,39 +383,15 @@ gatk4/germlinecnvcaller: gatk4/intervallisttobed: - modules/nf-core/gatk4/intervallisttobed/** - tests/modules/nf-core/gatk4/intervallisttobed/** -gatk4/learnreadorientationmodel: - - modules/nf-core/gatk4/learnreadorientationmodel/** - - tests/modules/nf-core/gatk4/learnreadorientationmodel/** -gatk4/leftalignandtrimvariants: - - modules/nf-core/gatk4/leftalignandtrimvariants/** - - tests/modules/nf-core/gatk4/leftalignandtrimvariants/** -gatk4/mergebamalignment: - - modules/nf-core/gatk4/mergebamalignment/** - - tests/modules/nf-core/gatk4/mergebamalignment/** gatk4/postprocessgermlinecnvcalls: - modules/nf-core/gatk4/postprocessgermlinecnvcalls/** - tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/** -gatk4/preprocessintervals: - - modules/nf-core/gatk4/preprocessintervals/** - - tests/modules/nf-core/gatk4/preprocessintervals/** -gatk4/printreads: - - modules/nf-core/gatk4/printreads/** - - tests/modules/nf-core/gatk4/printreads/** gatk4/printsvevidence: - modules/nf-core/gatk4/printsvevidence/** - tests/modules/nf-core/gatk4/printsvevidence/** -gatk4/revertsam: - - modules/nf-core/gatk4/revertsam/** - - tests/modules/nf-core/gatk4/revertsam/** -gatk4/samtofastq: - - modules/nf-core/gatk4/samtofastq/** - - tests/modules/nf-core/gatk4/samtofastq/** gatk4/selectsamples: - modules/nf-core/gatk4/selectsamples/** - tests/modules/nf-core/gatk4/selectsamples/** -gatk4/shiftfasta: - - modules/nf-core/gatk4/shiftfasta/** - - tests/modules/nf-core/gatk4/shiftfasta/** gatk4/sitedepthtobaf: - modules/nf-core/gatk4/sitedepthtobaf/** - tests/modules/nf-core/gatk4/sitedepthtobaf/** @@ -590,15 +488,6 @@ gridss/gridssgenerateponbedpe: gsea/gsea: - modules/nf-core/gsea/gsea/** - tests/modules/nf-core/gsea/gsea/** -gstama/collapse: - - modules/nf-core/gstama/collapse/** - - tests/modules/nf-core/gstama/collapse/** -gstama/merge: - - modules/nf-core/gstama/merge/** - - tests/modules/nf-core/gstama/merge/** -gstama/polyacleanup: - - modules/nf-core/gstama/polyacleanup/** - - tests/modules/nf-core/gstama/polyacleanup/** gubbins: - modules/nf-core/gubbins/** - tests/modules/nf-core/gubbins/** @@ -623,9 +512,6 @@ haplocheck: haplogrep2/classify: - modules/nf-core/haplogrep2/classify/** - tests/modules/nf-core/haplogrep2/classify/** -happy/sompy: - - modules/nf-core/happy/sompy/** - - tests/modules/nf-core/happy/sompy/** hicap: - modules/nf-core/hicap/** - tests/modules/nf-core/hicap/** @@ -1013,42 +899,15 @@ peka: phyloflash: - modules/nf-core/phyloflash/** - tests/modules/nf-core/phyloflash/** -picard/bedtointervallist: - - modules/nf-core/picard/bedtointervallist/** - - tests/modules/nf-core/picard/bedtointervallist/** -picard/cleansam: - - modules/nf-core/picard/cleansam/** - - tests/modules/nf-core/picard/cleansam/** picard/collectinsertsizemetrics: - modules/nf-core/picard/collectinsertsizemetrics/** - tests/modules/nf-core/picard/collectinsertsizemetrics/** -picard/collectmultiplemetrics: - - modules/nf-core/picard/collectmultiplemetrics/** - - tests/modules/nf-core/picard/collectmultiplemetrics/** picard/collectrnaseqmetrics: - modules/nf-core/picard/collectrnaseqmetrics/** - tests/modules/nf-core/picard/collectrnaseqmetrics/** -picard/fastqtosam: - - modules/nf-core/picard/fastqtosam/** - - tests/modules/nf-core/picard/fastqtosam/** picard/filtersamreads: - modules/nf-core/picard/filtersamreads/** - tests/modules/nf-core/picard/filtersamreads/** -picard/fixmateinformation: - - modules/nf-core/picard/fixmateinformation/** - - tests/modules/nf-core/picard/fixmateinformation/** -picard/liftovervcf: - - modules/nf-core/picard/liftovervcf/** - - tests/modules/nf-core/picard/liftovervcf/** -picard/renamesampleinvcf: - - modules/nf-core/picard/renamesampleinvcf/** - - tests/modules/nf-core/picard/renamesampleinvcf/** -picard/sortsam: - - modules/nf-core/picard/sortsam/** - - tests/modules/nf-core/picard/sortsam/** -picard/sortvcf: - - modules/nf-core/picard/sortvcf/** - - tests/modules/nf-core/picard/sortvcf/** pindel/pindel: - modules/nf-core/pindel/pindel/** - tests/modules/nf-core/pindel/pindel/** diff --git a/tests/modules/nf-core/bandage/image/main.nf b/tests/modules/nf-core/bandage/image/main.nf deleted file mode 100644 index 3da08d40bc0..00000000000 --- a/tests/modules/nf-core/bandage/image/main.nf +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BANDAGE_IMAGE } from '../../../../../modules/nf-core/bandage/image/main.nf' - -workflow test_bandage_image { - input = [ - [ id:'B-3106' ], // meta map - file( params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true) - ] - - BANDAGE_IMAGE ( input ) -} diff --git a/tests/modules/nf-core/bandage/image/nextflow.config b/tests/modules/nf-core/bandage/image/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/bandage/image/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/bandage/image/test.yml b/tests/modules/nf-core/bandage/image/test.yml deleted file mode 100644 index 07949fcd17c..00000000000 --- a/tests/modules/nf-core/bandage/image/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: bandage image - command: nextflow run ./tests/modules/nf-core/bandage/image -entry test_bandage_image -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bandage/image/nextflow.config - tags: - - bandage - - bandage/image - files: - - path: output/bandage/B-3106.png - - path: output/bandage/B-3106.svg diff --git a/tests/modules/nf-core/bbmap/bbnorm/main.nf b/tests/modules/nf-core/bbmap/bbnorm/main.nf deleted file mode 100644 index d0f65273280..00000000000 --- a/tests/modules/nf-core/bbmap/bbnorm/main.nf +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BBMAP_BBNORM } from '../../../../../modules/nf-core/bbmap/bbnorm/main.nf' - -workflow test_bbmap_bbnorm_se { - - input = [ - [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - - BBMAP_BBNORM ( input ) -} - -workflow test_bbmap_bbnorm_pe { - - input = [ - [ 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) - ] - ] - - BBMAP_BBNORM ( input ) -} - -workflow test_bbmap_bbnorm_interleaved { - - input = [ - [id:'test', single_end:true ], - [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true)] - ] - - BBMAP_BBNORM ( input ) -} - - workflow test_bbmap_bbnorm_multiple_input { - input = [ - [id:'test', single_end:true ], - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) - ] - ] - - BBMAP_BBNORM ( input ) -} diff --git a/tests/modules/nf-core/bbmap/bbnorm/nextflow.config b/tests/modules/nf-core/bbmap/bbnorm/nextflow.config deleted file mode 100644 index 40716de692c..00000000000 --- a/tests/modules/nf-core/bbmap/bbnorm/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.args = 'target=100 min=5' -} diff --git a/tests/modules/nf-core/bbmap/bbnorm/test.yml b/tests/modules/nf-core/bbmap/bbnorm/test.yml deleted file mode 100644 index c5c15edc783..00000000000 --- a/tests/modules/nf-core/bbmap/bbnorm/test.yml +++ /dev/null @@ -1,30 +0,0 @@ -- name: bbmap bbnorm test_bbmap_bbnorm_se - command: nextflow run ./tests/modules/nf-core/bbmap/bbnorm -entry test_bbmap_bbnorm_se -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbnorm/nextflow.config - tags: - - bbmap/bbnorm - - bbmap - files: - - path: output/bbmap/test.bbnorm.log - - path: output/bbmap/test.fastq.gz - - path: output/bbmap/versions.yml - -- name: bbmap bbnorm test_bbmap_bbnorm_pe - command: nextflow run ./tests/modules/nf-core/bbmap/bbnorm -entry test_bbmap_bbnorm_pe -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbnorm/nextflow.config - tags: - - bbmap/bbnorm - - bbmap - files: - - path: output/bbmap/test.bbnorm.log - - path: output/bbmap/test_1.nm.fastq.gz - - path: output/bbmap/test_2.nm.fastq.gz - - path: output/bbmap/versions.yml - -- name: bbmap bbnorm test_bbmap_bbnorm_interleaved - command: nextflow run ./tests/modules/nf-core/bbmap/bbnorm -entry test_bbmap_bbnorm_interleaved -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbnorm/nextflow.config - tags: - - bbmap/bbnorm - - bbmap - files: - - path: output/bbmap/test.bbnorm.log - - path: output/bbmap/test.fastq.gz - - path: output/bbmap/versions.yml diff --git a/tests/modules/nf-core/bbmap/index/main.nf b/tests/modules/nf-core/bbmap/index/main.nf deleted file mode 100644 index 1c1ad0f422e..00000000000 --- a/tests/modules/nf-core/bbmap/index/main.nf +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BBMAP_INDEX } from '../../../../../modules/nf-core/bbmap/index/main.nf' - -workflow test_bbmap_index { - - input = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - - BBMAP_INDEX ( input ) -} diff --git a/tests/modules/nf-core/bbmap/index/nextflow.config b/tests/modules/nf-core/bbmap/index/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/bbmap/index/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/bbmap/index/test.yml b/tests/modules/nf-core/bbmap/index/test.yml deleted file mode 100644 index d9956fabca4..00000000000 --- a/tests/modules/nf-core/bbmap/index/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: bbmap index - command: nextflow run ./tests/modules/nf-core/bbmap/index -entry test_bbmap_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/index/nextflow.config - tags: - - bbmap - - bbmap/index - files: - - path: output/bbmap/ref/genome/1/chr1.chrom.gz - - path: output/bbmap/ref/index/1/chr1_index_k13_c15_b1.block - md5sum: 9f0d9a7413c1d2c16cc24555b2381163 diff --git a/tests/modules/nf-core/bbmap/pileup/main.nf b/tests/modules/nf-core/bbmap/pileup/main.nf deleted file mode 100644 index beb482abfce..00000000000 --- a/tests/modules/nf-core/bbmap/pileup/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BBMAP_PILEUP } from '../../../../../modules/nf-core/bbmap/pileup/main.nf' - -workflow test_bbmap_pileup { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - BBMAP_PILEUP ( input ) -} diff --git a/tests/modules/nf-core/bbmap/pileup/nextflow.config b/tests/modules/nf-core/bbmap/pileup/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/bbmap/pileup/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/bbmap/pileup/test.yml b/tests/modules/nf-core/bbmap/pileup/test.yml deleted file mode 100644 index befee77155f..00000000000 --- a/tests/modules/nf-core/bbmap/pileup/test.yml +++ /dev/null @@ -1,12 +0,0 @@ -- name: "bbmap pileup" - command: nextflow run ./tests/modules/nf-core/bbmap/pileup -entry test_bbmap_pileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/pileup/nextflow.config - tags: - - "bbmap" - - "bbmap/pileup" - files: - - path: "output/bbmap/test.coverage.stats.txt" - md5sum: c3fc9d0681589b69e3301ca3cb27b7a4 - - path: "output/bbmap/test.coverage.hist.txt" - md5sum: 96915920ef42ddc9483457dd4585a088 - - path: output/bbmap/versions.yml - md5sum: 20fc1f456119714e10196c62f6d04be4 diff --git a/tests/modules/nf-core/bcftools/roh/main.nf b/tests/modules/nf-core/bcftools/roh/main.nf deleted file mode 100644 index d18a0aecefc..00000000000 --- a/tests/modules/nf-core/bcftools/roh/main.nf +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BCFTOOLS_ROH } from '../../../../../modules/nf-core/bcftools/roh/main.nf' - -workflow test_bcftools_roh { - - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - af_file = [[],[]] - gen_map = [] - regions = [] - targets = [] - samples = [] - - BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets ) -} - -workflow test_bcftools_roh_stub { - - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - af_file = [[],[]] - gen_map = [] - regions = [] - targets = [] - samples = [] - - BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets ) -} diff --git a/tests/modules/nf-core/bcftools/roh/nextflow.config b/tests/modules/nf-core/bcftools/roh/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/bcftools/roh/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/bcftools/roh/test.yml b/tests/modules/nf-core/bcftools/roh/test.yml deleted file mode 100644 index 3ea272dd53a..00000000000 --- a/tests/modules/nf-core/bcftools/roh/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: "bcftools roh" - command: nextflow run ./tests/modules/nf-core/bcftools/roh -entry test_bcftools_roh -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/roh/nextflow.config - tags: - - "bcftools" - - "bcftools/roh" - files: - - path: "output/bcftools/test.roh" - - path: "output/bcftools/versions.yml" - -- name: "bcftools roh stub" - command: nextflow run ./tests/modules/nf-core/bcftools/roh -entry test_bcftools_roh_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/roh/nextflow.config - tags: - - "bcftools" - - "bcftools/roh" - files: - - path: "output/bcftools/test.roh" - - path: "output/bcftools/versions.yml" diff --git a/tests/modules/nf-core/bcftools/split/main.nf b/tests/modules/nf-core/bcftools/split/main.nf deleted file mode 100644 index 6304841ca82..00000000000 --- a/tests/modules/nf-core/bcftools/split/main.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BCFTOOLS_SPLIT } from '../../../../../modules/nf-core/bcftools/split/main.nf' - -workflow test_bcftools_split { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) - ] - - BCFTOOLS_SPLIT ( input ) -} diff --git a/tests/modules/nf-core/bcftools/split/nextflow.config b/tests/modules/nf-core/bcftools/split/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/bcftools/split/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/bcftools/split/test.yml b/tests/modules/nf-core/bcftools/split/test.yml deleted file mode 100644 index d4178a52b41..00000000000 --- a/tests/modules/nf-core/bcftools/split/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: bcftools split test_bcftools_split - command: nextflow run ./tests/modules/nf-core/bcftools/split -entry test_bcftools_split -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/split/nextflow.config - tags: - - bcftools - - bcftools/split - files: - - path: output/bcftools/test.chr22.vcf.gz - - path: output/bcftools/versions.yml diff --git a/tests/modules/nf-core/beagle5/beagle/main.nf b/tests/modules/nf-core/beagle5/beagle/main.nf deleted file mode 100644 index b54d2b13e02..00000000000 --- a/tests/modules/nf-core/beagle5/beagle/main.nf +++ /dev/null @@ -1,47 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEAGLE5_BEAGLE } from '../../../../../modules/nf-core/beagle5/beagle/main.nf' - -workflow test_beagle5_beagle { - - input = [ - [ id:'test', single_end:false ], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true) - ] - refpanel = [] - genmap = [] - exclsamples = [] - exclmarkers = [] - - BEAGLE5_BEAGLE ( input, refpanel, genmap, exclsamples, exclmarkers ) -} - -workflow test_beagle5_beagle_ref { - - input = [ - [ id:'test', single_end:false ], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true) - ] - refpanel = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/ref.22Jul22.46e.vcf.gz", checkIfExists: true) - genmap = [] - exclsamples = [] - exclmarkers = [] - - BEAGLE5_BEAGLE ( input, refpanel, genmap, exclsamples, exclmarkers ) -} - -workflow test_beagle5_beagle_ref_map { - - input = [ - [ id:'test', single_end:false ], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true) - ] - refpanel = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/ref.22Jul22.46e.vcf.gz", checkIfExists: true) - genmap = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/plink.chr22.GRCh38.map", checkIfExists: true) - exclsamples = [] - exclmarkers = [] - - BEAGLE5_BEAGLE ( input, refpanel, genmap, exclsamples, exclmarkers ) -} diff --git a/tests/modules/nf-core/beagle5/beagle/nextflow.config b/tests/modules/nf-core/beagle5/beagle/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/beagle5/beagle/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/beagle5/beagle/test.yml b/tests/modules/nf-core/beagle5/beagle/test.yml deleted file mode 100644 index 4d7831c3558..00000000000 --- a/tests/modules/nf-core/beagle5/beagle/test.yml +++ /dev/null @@ -1,32 +0,0 @@ -- name: beagle5 beagle test_beagle5_beagle - command: nextflow run ./tests/modules/nf-core/beagle5/beagle -entry test_beagle5_beagle -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/beagle5/beagle/nextflow.config - tags: - - beagle5 - - beagle5/beagle - files: - - path: output/beagle5/test.bglout.log - contains: ["Brian L. Browning"] - - path: output/beagle5/test.bglout.vcf.gz - md5sum: 14e622330da1749c77d5b488b76842cc - -- name: beagle5 beagle test_beagle5_beagle_ref - command: nextflow run ./tests/modules/nf-core/beagle5/beagle -entry test_beagle5_beagle_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/beagle5/beagle/nextflow.config - tags: - - beagle5 - - beagle5/beagle - files: - - path: output/beagle5/test.bglout.log - contains: ["Brian L. Browning"] - - path: output/beagle5/test.bglout.vcf.gz - md5sum: 1c2dbf11ede60ac2f2e16b02e5351f3d - -- name: beagle5 beagle test_beagle5_beagle_ref_map - command: nextflow run ./tests/modules/nf-core/beagle5/beagle -entry test_beagle5_beagle_ref_map -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/beagle5/beagle/nextflow.config - tags: - - beagle5 - - beagle5/beagle - files: - - path: output/beagle5/test.bglout.log - contains: ["Brian L. Browning"] - - path: output/beagle5/test.bglout.vcf.gz - md5sum: 1c9f97b269542c0e632c47d854a74457 diff --git a/tests/modules/nf-core/bedtools/groupby/main.nf b/tests/modules/nf-core/bedtools/groupby/main.nf deleted file mode 100644 index f76256c4b19..00000000000 --- a/tests/modules/nf-core/bedtools/groupby/main.nf +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_GROUPBY } from '../../../../../modules/nf-core/bedtools/groupby/main.nf' - -workflow test_bedtools_groupby { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), - ] - BEDTOOLS_GROUPBY ( input, 5 ) -} diff --git a/tests/modules/nf-core/bedtools/groupby/nextflow.config b/tests/modules/nf-core/bedtools/groupby/nextflow.config deleted file mode 100644 index 97db8a6c3f0..00000000000 --- a/tests/modules/nf-core/bedtools/groupby/nextflow.config +++ /dev/null @@ -1,10 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - - withName: BEDTOOLS_GROUPBY { - ext.args = "-g 1" - } - -} diff --git a/tests/modules/nf-core/bedtools/groupby/test.yml b/tests/modules/nf-core/bedtools/groupby/test.yml deleted file mode 100644 index ab0f437dcac..00000000000 --- a/tests/modules/nf-core/bedtools/groupby/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: bedtools groupby test_bedtools_groupby - command: nextflow run ./tests/modules/nf-core/bedtools/groupby -entry test_bedtools_groupby -c ./tests/config/nextflow.config - tags: - - bedtools - - bedtools/groupby - files: - - path: output/bedtools/test.grouped.bed - md5sum: ba080b3d282f206f6312122c71a66745 - - path: output/bedtools/versions.yml diff --git a/tests/modules/nf-core/bedtools/jaccard/main.nf b/tests/modules/nf-core/bedtools/jaccard/main.nf deleted file mode 100644 index 97823041cc3..00000000000 --- a/tests/modules/nf-core/bedtools/jaccard/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_JACCARD } from '../../../../../modules/nf-core/bedtools/jaccard/main.nf' - -workflow test_bedtools_jaccard { - - 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) - ] - - BEDTOOLS_JACCARD ( input, [[],[]] ) -} - -workflow test_bedtools_jaccard_genome { - - 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) - ] - - genome = [ - [ id:'genome' ], - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - - BEDTOOLS_JACCARD ( input, genome ) -} diff --git a/tests/modules/nf-core/bedtools/jaccard/nextflow.config b/tests/modules/nf-core/bedtools/jaccard/nextflow.config deleted file mode 100644 index 499fa9974b3..00000000000 --- a/tests/modules/nf-core/bedtools/jaccard/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: "test_bedtools_jaccard_genome:BEDTOOLS_JACCARD" { - ext.args = "-sorted" - } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/bedtools/jaccard/test.yml b/tests/modules/nf-core/bedtools/jaccard/test.yml deleted file mode 100644 index 0368fc92217..00000000000 --- a/tests/modules/nf-core/bedtools/jaccard/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: bedtools jaccard test_bedtools_jaccard - command: nextflow run ./tests/modules/nf-core/bedtools/jaccard -entry test_bedtools_jaccard -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/jaccard/nextflow.config - tags: - - bedtools/jaccard - - bedtools - files: - - path: output/bedtools/test.tsv - md5sum: b737742026a3b512a494f3aa7935fded - - path: output/bedtools/versions.yml - -- name: bedtools jaccard test_bedtools_jaccard_genome - command: nextflow run ./tests/modules/nf-core/bedtools/jaccard -entry test_bedtools_jaccard_genome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/jaccard/nextflow.config - tags: - - bedtools/jaccard - - bedtools - files: - - path: output/bedtools/test.tsv - md5sum: b737742026a3b512a494f3aa7935fded - - path: output/bedtools/versions.yml diff --git a/tests/modules/nf-core/bedtools/makewindows/main.nf b/tests/modules/nf-core/bedtools/makewindows/main.nf deleted file mode 100644 index 13b59ea54e1..00000000000 --- a/tests/modules/nf-core/bedtools/makewindows/main.nf +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_MAKEWINDOWS } from '../../../../../modules/nf-core/bedtools/makewindows/main.nf' - -workflow test_bedtools_makewindows_bed { - - input = [ - [ id:'test2'], - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - - BEDTOOLS_MAKEWINDOWS ( input ) -} - -workflow test_bedtools_makewindows_fai { - - input = [ - [ id:'test2'], - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - - BEDTOOLS_MAKEWINDOWS ( input ) -} diff --git a/tests/modules/nf-core/bedtools/makewindows/nextflow.config b/tests/modules/nf-core/bedtools/makewindows/nextflow.config deleted file mode 100644 index e8b8c3eae29..00000000000 --- a/tests/modules/nf-core/bedtools/makewindows/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: BEDTOOLS_MAKEWINDOWS { - ext.args = '-w 50 ' - } - -} diff --git a/tests/modules/nf-core/bedtools/makewindows/test.yml b/tests/modules/nf-core/bedtools/makewindows/test.yml deleted file mode 100644 index f286c65abaa..00000000000 --- a/tests/modules/nf-core/bedtools/makewindows/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: bedtools makewindows test_bedtools_makewindows_bed - command: nextflow run ./tests/modules/nf-core/bedtools/makewindows -entry test_bedtools_makewindows_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/makewindows/nextflow.config - tags: - - bedtools/makewindows - - bedtools - files: - - path: output/bedtools/test2.bed - md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e - - path: output/bedtools/versions.yml - -- name: bedtools makewindows test_bedtools_makewindows_fai - command: nextflow run ./tests/modules/nf-core/bedtools/makewindows -entry test_bedtools_makewindows_fai -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/makewindows/nextflow.config - tags: - - bedtools/makewindows - - bedtools - files: - - path: output/bedtools/test2.bed - md5sum: 622d1f62786fe4239b76c53168f21c54 - - path: output/bedtools/versions.yml diff --git a/tests/modules/nf-core/bedtools/maskfasta/main.nf b/tests/modules/nf-core/bedtools/maskfasta/main.nf deleted file mode 100644 index 115a44e6b6e..00000000000 --- a/tests/modules/nf-core/bedtools/maskfasta/main.nf +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_MASKFASTA } from '../../../../../modules/nf-core/bedtools/maskfasta/main.nf' - -workflow test_bedtools_maskfasta { - bed = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - - BEDTOOLS_MASKFASTA ( bed, fasta ) -} diff --git a/tests/modules/nf-core/bedtools/maskfasta/nextflow.config b/tests/modules/nf-core/bedtools/maskfasta/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/bedtools/maskfasta/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/bedtools/maskfasta/test.yml b/tests/modules/nf-core/bedtools/maskfasta/test.yml deleted file mode 100644 index 62c834a8c09..00000000000 --- a/tests/modules/nf-core/bedtools/maskfasta/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: bedtools maskfasta - command: nextflow run ./tests/modules/nf-core/bedtools/maskfasta -entry test_bedtools_maskfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/maskfasta/nextflow.config - tags: - - bedtools - - bedtools/maskfasta - files: - - path: ./output/bedtools/test.fa - md5sum: f4f6749698f11074228d2c79338e3b9c diff --git a/tests/modules/nf-core/bedtools/multiinter/main.nf b/tests/modules/nf-core/bedtools/multiinter/main.nf deleted file mode 100644 index b453116857c..00000000000 --- a/tests/modules/nf-core/bedtools/multiinter/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_MULTIINTER } from '../../../../../modules/nf-core/bedtools/multiinter/main.nf' - -workflow test_bedtools_multiinter { - - input = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true) - ] - ] - - BEDTOOLS_MULTIINTER ( input, [] ) -} - -workflow test_bedtools_multiinter_genome { - - input = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true) - ] - ] - sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) - - BEDTOOLS_MULTIINTER ( input, sizes ) -} diff --git a/tests/modules/nf-core/bedtools/multiinter/nextflow.config b/tests/modules/nf-core/bedtools/multiinter/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/bedtools/multiinter/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/bedtools/multiinter/test.yml b/tests/modules/nf-core/bedtools/multiinter/test.yml deleted file mode 100644 index 16e7bca6636..00000000000 --- a/tests/modules/nf-core/bedtools/multiinter/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: bedtools multiinter test_bedtools_multiinter - command: nextflow run ./tests/modules/nf-core/bedtools/multiinter -entry test_bedtools_multiinter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/multiinter/nextflow.config - tags: - - bedtools/multiinter - - bedtools - files: - - path: output/bedtools/test.bed - md5sum: 03d8d889a19cf26e038868775bbcbaa7 - - path: output/bedtools/versions.yml - -- name: bedtools multiinter test_bedtools_multiinter_genome - command: nextflow run ./tests/modules/nf-core/bedtools/multiinter -entry test_bedtools_multiinter_genome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/multiinter/nextflow.config - tags: - - bedtools/multiinter - - bedtools - files: - - path: output/bedtools/test.bed - md5sum: 03d8d889a19cf26e038868775bbcbaa7 - - path: output/bedtools/versions.yml diff --git a/tests/modules/nf-core/bedtools/shift/main.nf b/tests/modules/nf-core/bedtools/shift/main.nf deleted file mode 100644 index e4453c85367..00000000000 --- a/tests/modules/nf-core/bedtools/shift/main.nf +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_SHIFT } from '../../../../../modules/nf-core/bedtools/shift/main.nf' - -workflow test_bedtools_shift { - input = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - sizes = [[id:'sizes'],file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)] - BEDTOOLS_SHIFT ( input, sizes ) -} diff --git a/tests/modules/nf-core/bedtools/shift/test.yml b/tests/modules/nf-core/bedtools/shift/test.yml deleted file mode 100644 index 820eb95a042..00000000000 --- a/tests/modules/nf-core/bedtools/shift/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: bedtools shift - command: nextflow run ./tests/modules/nf-core/bedtools/shift -entry test_bedtools_shift -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/shift/nextflow.config - tags: - - bedtools - - bedtools/shift - files: - - path: ./output/bedtools/test_out.bed - md5sum: fdfa2c33084f1f8e42505076a449afdc diff --git a/tests/modules/nf-core/bedtools/slop/main.nf b/tests/modules/nf-core/bedtools/slop/main.nf deleted file mode 100644 index 40531695034..00000000000 --- a/tests/modules/nf-core/bedtools/slop/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_SLOP } from '../../../../../modules/nf-core/bedtools/slop/main.nf' - -workflow test_bedtools_slop { - input = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) - - BEDTOOLS_SLOP ( input, sizes ) -} - diff --git a/tests/modules/nf-core/bedtools/slop/test.yml b/tests/modules/nf-core/bedtools/slop/test.yml deleted file mode 100644 index a69dedb6317..00000000000 --- a/tests/modules/nf-core/bedtools/slop/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: bedtools slop - command: nextflow run ./tests/modules/nf-core/bedtools/slop -entry test_bedtools_slop -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/slop/nextflow.config - tags: - - bedtools - - bedtools/slop - files: - - path: ./output/bedtools/test_out.bed - md5sum: 4f1d8924925fe5d205c9e1981fe290a4 diff --git a/tests/modules/nf-core/bedtools/split/main.nf b/tests/modules/nf-core/bedtools/split/main.nf deleted file mode 100644 index 686d251cc96..00000000000 --- a/tests/modules/nf-core/bedtools/split/main.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_SPLIT } from '../../../../../modules/nf-core/bedtools/split/main.nf' - -workflow test_bedtools_split { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true), - 2 - ] - - BEDTOOLS_SPLIT ( input ) -} diff --git a/tests/modules/nf-core/bedtools/split/nextflow.config b/tests/modules/nf-core/bedtools/split/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/bedtools/split/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/bedtools/split/test.yml b/tests/modules/nf-core/bedtools/split/test.yml deleted file mode 100644 index efb7065ba9b..00000000000 --- a/tests/modules/nf-core/bedtools/split/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: bedtools split test_bedtools_split - command: nextflow run ./tests/modules/nf-core/bedtools/split -entry test_bedtools_split -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/split/nextflow.config - tags: - - bedtools/split - - bedtools - files: - - path: output/bedtools/test.00001.bed - - path: output/bedtools/test.00002.bed - - path: output/bedtools/versions.yml diff --git a/tests/modules/nf-core/bedtools/subtract/main.nf b/tests/modules/nf-core/bedtools/subtract/main.nf deleted file mode 100644 index a86c81a1870..00000000000 --- a/tests/modules/nf-core/bedtools/subtract/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_SUBTRACT } from '../../../../../modules/nf-core/bedtools/subtract/main.nf' - -workflow test_bedtools_subtract { - input = [ - [ id:'test_subtract' ], - file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - - BEDTOOLS_SUBTRACT ( input ) -} diff --git a/tests/modules/nf-core/bedtools/subtract/nextflow.config b/tests/modules/nf-core/bedtools/subtract/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/bedtools/subtract/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/bedtools/subtract/test.yml b/tests/modules/nf-core/bedtools/subtract/test.yml deleted file mode 100644 index efb1863cbaa..00000000000 --- a/tests/modules/nf-core/bedtools/subtract/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: bedtools subtract - command: nextflow run ./tests/modules/nf-core/bedtools/subtract -entry test_bedtools_subtract -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/subtract/nextflow.config - tags: - - bedtools - - bedtools/subtract - files: - - path: output/bedtools/test_subtract.bed - md5sum: 63513c4dc69e8b481ce3b4b2a9f24259 diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf deleted file mode 100644 index b308871657b..00000000000 --- a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK_UNIFIEDGENOTYPER } from '../../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf' - -workflow test_gatk_unifiedgenotyper { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - ] - fasta = [ - [id: 'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - fai = [ - [id: 'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - dict = [ - [id: 'test'], - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - ] - - GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [[],[]], [[],[]], [[],[]], [[],[]]) -} diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config b/tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/gatk/unifiedgenotyper/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/gatk/unifiedgenotyper/test.yml b/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml deleted file mode 100644 index 9350e5a6af6..00000000000 --- a/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: gatk unifiedgenotyper test_gatk_unifiedgenotyper - command: nextflow run ./tests/modules/nf-core/gatk/unifiedgenotyper -entry test_gatk_unifiedgenotyper -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config - tags: - - gatk - - gatk/unifiedgenotyper - files: - - path: output/gatk/test.vcf.gz - contains: - - "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test" diff --git a/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf deleted file mode 100644 index 29b149b2cd9..00000000000 --- a/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ /dev/null @@ -1,82 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../../modules/nf-core/gatk4/calibratedragstrmodel/main.nf' - -workflow test_gatk4_calibratedragstrmodel_bam { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true) - - GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile ) -} - -workflow test_gatk4_calibratedragstrmodel_cram { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true) - - GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile ) -} - -workflow test_gatk4_calibratedragstrmodel_beds { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true) - - GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile ) -} - -workflow test_gatk4_calibratedragstrmodel_gzipped_beds { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true) - - GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile ) -} - diff --git a/tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config b/tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/gatk4/calibratedragstrmodel/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/gatk4/calibratedragstrmodel/test.yml b/tests/modules/nf-core/gatk4/calibratedragstrmodel/test.yml deleted file mode 100644 index 60a33dc1c92..00000000000 --- a/tests/modules/nf-core/gatk4/calibratedragstrmodel/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_bam - command: nextflow run ./tests/modules/nf-core/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config - tags: - - gatk4/calibratedragstrmodel - - gatk4 - files: - - path: output/gatk4/test.txt - md5sum: e16fa32906c74bb18b93e98a86718ff1 - - path: output/gatk4/versions.yml - -- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_cram - command: nextflow run ./tests/modules/nf-core/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config - tags: - - gatk4/calibratedragstrmodel - - gatk4 - files: - - path: output/gatk4/test.txt - md5sum: 81c7bf338886cb4d5c2cc07fc56afe44 - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/main.nf b/tests/modules/nf-core/gatk4/collectreadcounts/main.nf deleted file mode 100644 index 2ddc184a236..00000000000 --- a/tests/modules/nf-core/gatk4/collectreadcounts/main.nf +++ /dev/null @@ -1,54 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' - -workflow test_gatk4_collectreadcounts_hdf5 { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true), - ] - - fasta = [[],[]] - fai = [[],[]] - dict = [[],[]] - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) -} - -workflow test_gatk4_collectreadcounts_tsv { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true), - ] - - fasta = [[],[]] - fai = [[],[]] - dict = [[],[]] - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) -} - -workflow test_gatk4_collectreadcounts_cram { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true), - ] - - fasta = [[id:'test'], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - fai = [[id:'test'], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)] - dict = [[id:'test'], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) -} - diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config b/tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config deleted file mode 100644 index 3863bf92946..00000000000 --- a/tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config +++ /dev/null @@ -1,17 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: 'test_gatk4_collectreadcounts_hdf5:GATK4_COLLECTREADCOUNTS'{ - ext.args = "--interval-merging-rule OVERLAPPING_ONLY" - } - - withName: 'test_gatk4_collectreadcounts_tsv:GATK4_COLLECTREADCOUNTS' { - ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" - } - - withName: 'test_gatk4_collectreadcounts_cram:GATK4_COLLECTREADCOUNTS' { - ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" - } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/test.yml b/tests/modules/nf-core/gatk4/collectreadcounts/test.yml deleted file mode 100644 index cc0f2106d3c..00000000000 --- a/tests/modules/nf-core/gatk4/collectreadcounts/test.yml +++ /dev/null @@ -1,54 +0,0 @@ -- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_hdf5 - command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_hdf5 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config - tags: - - gatk4/collectreadcounts - - gatk4 - files: - - path: output/gatk4/test.hdf5 - - path: output/gatk4/versions.yml - -- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_tsv - command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_tsv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config - tags: - - gatk4/collectreadcounts - - gatk4 - files: - - path: output/gatk4/test.tsv - md5sum: 8e45a6164916c303387f39f02ce45841 - - path: output/gatk4/versions.yml - -- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_cram - command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config - tags: - - gatk4/collectreadcounts - - gatk4 - files: - - path: output/gatk4/test.tsv - - path: output/gatk4/versions.yml - -- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_hdf5_stub - command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_hdf5 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config -stub - tags: - - gatk4/collectreadcounts - - gatk4 - files: - - path: output/gatk4/test.hdf5 - - path: output/gatk4/versions.yml - -- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_tsv_stub - command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_tsv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config -stub - tags: - - gatk4/collectreadcounts - - gatk4 - files: - - path: output/gatk4/test.tsv - - path: output/gatk4/versions.yml - -- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_cram_stub - command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config -stub - tags: - - gatk4/collectreadcounts - - gatk4 - files: - - path: output/gatk4/test.tsv - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/main.nf b/tests/modules/nf-core/gatk4/collectsvevidence/main.nf deleted file mode 100644 index 68f406bd560..00000000000 --- a/tests/modules/nf-core/gatk4/collectsvevidence/main.nf +++ /dev/null @@ -1,56 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_COLLECTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' - -workflow test_gatk4_collectsvevidence_cram { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - [], - [] - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict ) -} - -workflow test_gatk4_collectsvevidence_bam { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - [], - [] - ] - - fasta = [] - fasta_fai = [] - dict = [] - - GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict ) -} - -workflow test_gatk4_collectsvevidence_allele_count { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) - ] - - fasta = [] - fasta_fai = [] - dict = [] - - GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict ) -} diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config b/tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config deleted file mode 100644 index 08bbbe32685..00000000000 --- a/tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GATK4_COLLECTSVEVIDENCE { - ext.args = "--sample-name normal" - } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/test.yml b/tests/modules/nf-core/gatk4/collectsvevidence/test.yml deleted file mode 100644 index 9032e7f0cf3..00000000000 --- a/tests/modules/nf-core/gatk4/collectsvevidence/test.yml +++ /dev/null @@ -1,51 +0,0 @@ -- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_cram - command: nextflow run ./tests/modules/nf-core/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config - tags: - - gatk4/collectsvevidence - - gatk4 - files: - - path: output/gatk4/test.pe.txt.gz - md5sum: 19f13dd0408204590b40239d14acbdde - - path: output/gatk4/test.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/test.sr.txt.gz - md5sum: fb9ce52193a0db3a084890bd6bbf6a64 - - path: output/gatk4/test.sr.txt.gz.tbi - md5sum: 33b3a9ff444eb0e0fc3016239651f05f - - path: output/gatk4/versions.yml - -- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_bam - command: nextflow run ./tests/modules/nf-core/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config - tags: - - gatk4/collectsvevidence - - gatk4 - files: - - path: output/gatk4/test.pe.txt.gz - md5sum: 19f13dd0408204590b40239d14acbdde - - path: output/gatk4/test.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/test.sr.txt.gz - md5sum: fb9ce52193a0db3a084890bd6bbf6a64 - - path: output/gatk4/test.sr.txt.gz.tbi - md5sum: 33b3a9ff444eb0e0fc3016239651f05f - - path: output/gatk4/versions.yml - -- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_allele_count - command: nextflow run ./tests/modules/nf-core/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_allele_count -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config - tags: - - gatk4/collectsvevidence - - gatk4 - files: - - path: output/gatk4/test.pe.txt.gz - md5sum: 19f13dd0408204590b40239d14acbdde - - path: output/gatk4/test.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/test.sd.txt.gz - md5sum: 1d1f4e95ee036020a0e5d41dbf114cd7 - - path: output/gatk4/test.sd.txt.gz.tbi - md5sum: 2eafe78041c60b0d6b9b077dd88eb3ee - - path: output/gatk4/test.sr.txt.gz - md5sum: fb9ce52193a0db3a084890bd6bbf6a64 - - path: output/gatk4/test.sr.txt.gz.tbi - md5sum: 33b3a9ff444eb0e0fc3016239651f05f - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/composestrtablefile/main.nf b/tests/modules/nf-core/gatk4/composestrtablefile/main.nf deleted file mode 100644 index 4c62f05de88..00000000000 --- a/tests/modules/nf-core/gatk4/composestrtablefile/main.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_COMPOSESTRTABLEFILE } from '../../../../../modules/nf-core/gatk4/composestrtablefile/main.nf' - -workflow test_gatk4_composestrtablefile { - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - GATK4_COMPOSESTRTABLEFILE ( fasta, fasta_fai, dict ) -} diff --git a/tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config b/tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/gatk4/composestrtablefile/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/gatk4/composestrtablefile/test.yml b/tests/modules/nf-core/gatk4/composestrtablefile/test.yml deleted file mode 100644 index 9af011197f5..00000000000 --- a/tests/modules/nf-core/gatk4/composestrtablefile/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: gatk4 composestrtablefile test_gatk4_composestrtablefile - command: nextflow run ./tests/modules/nf-core/gatk4/composestrtablefile -entry test_gatk4_composestrtablefile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config - tags: - - gatk4/composestrtablefile - - gatk4 - files: - - path: output/gatk4/genome.zip - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/condensedepthevidence/main.nf b/tests/modules/nf-core/gatk4/condensedepthevidence/main.nf deleted file mode 100644 index dc3c89640f7..00000000000 --- a/tests/modules/nf-core/gatk4/condensedepthevidence/main.nf +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_CONDENSEDEPTHEVIDENCE } from '../../../../../modules/nf-core/gatk4/condensedepthevidence/main.nf' - -workflow test_gatk4_condensdepthevidence { - - input = [ - [ id:'test', single_end:false ], // meta map - file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true), - file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz.tbi", checkIfExists: true) - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - GATK4_CONDENSEDEPTHEVIDENCE ( - input, - fasta, - fasta_fai, - dict - ) -} diff --git a/tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config b/tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/gatk4/condensedepthevidence/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/gatk4/condensedepthevidence/test.yml b/tests/modules/nf-core/gatk4/condensedepthevidence/test.yml deleted file mode 100644 index 671d81dcab0..00000000000 --- a/tests/modules/nf-core/gatk4/condensedepthevidence/test.yml +++ /dev/null @@ -1,11 +0,0 @@ -- name: gatk4 condensedepthevidence test_gatk4_condensdepthevidence - command: nextflow run ./tests/modules/nf-core/gatk4/condensedepthevidence -entry test_gatk4_condensdepthevidence -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config - tags: - - gatk4 - - gatk4/condensedepthevidence - files: - - path: output/gatk4/test.rd.txt.gz - md5sum: c6c04b78f2aa40744f267518b3cb21b8 - - path: output/gatk4/test.rd.txt.gz.tbi - md5sum: c30d5548ad94063b105e227483b68779 - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/fastqtosam/main.nf b/tests/modules/nf-core/gatk4/fastqtosam/main.nf deleted file mode 100644 index 0a3aef644d4..00000000000 --- a/tests/modules/nf-core/gatk4/fastqtosam/main.nf +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_FASTQTOSAM } from '../../../../../modules/nf-core/gatk4/fastqtosam/main.nf' - -workflow test_gatk4_fastqtosam_single_end { - input = [ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - - GATK4_FASTQTOSAM ( input ) -} - -workflow test_gatk4_fastqtosam_paired_end { - input = [ [ 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) - ] - - GATK4_FASTQTOSAM ( input ) -} diff --git a/tests/modules/nf-core/gatk4/fastqtosam/nextflow.config b/tests/modules/nf-core/gatk4/fastqtosam/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/gatk4/fastqtosam/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/gatk4/fastqtosam/test.yml b/tests/modules/nf-core/gatk4/fastqtosam/test.yml deleted file mode 100644 index 482284d5956..00000000000 --- a/tests/modules/nf-core/gatk4/fastqtosam/test.yml +++ /dev/null @@ -1,16 +0,0 @@ -- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end - command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config - tags: - - gatk4 - - gatk4/fastqtosam - files: - - path: output/gatk4/test.bam - -- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end - command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config - tags: - - gatk4 - - gatk4/fastqtosam - files: - - path: output/gatk4/test.bam - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/filterintervals/main.nf b/tests/modules/nf-core/gatk4/filterintervals/main.nf deleted file mode 100644 index 9b45cf5925b..00000000000 --- a/tests/modules/nf-core/gatk4/filterintervals/main.nf +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_FILTERINTERVALS } from '../../../../../modules/nf-core/gatk4/filterintervals/main.nf' - -workflow test_gatk4_filterintervals { - - intervals = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_preprocessed_interval_list'], checkIfExists: true) - ] - read_counts = [[:],[file(params.test_data['homo_sapiens']['genome']['genome_preprocessed_count_tsv'], checkIfExists: true)]] - annotated_intervals = [[:],file(params.test_data['homo_sapiens']['genome']['genome_annotated_interval_tsv'], checkIfExists: true)] - - GATK4_FILTERINTERVALS ( intervals, read_counts, annotated_intervals ) -} diff --git a/tests/modules/nf-core/gatk4/filterintervals/test.yml b/tests/modules/nf-core/gatk4/filterintervals/test.yml deleted file mode 100644 index 792e07d2426..00000000000 --- a/tests/modules/nf-core/gatk4/filterintervals/test.yml +++ /dev/null @@ -1,16 +0,0 @@ -- name: gatk4 filterintervals test_gatk4_filterintervals - command: nextflow run ./tests/modules/nf-core/gatk4/filterintervals -entry test_gatk4_filterintervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filterintervals/nextflow.config - tags: - - gatk4/filterintervals - - gatk4 - files: - - path: output/gatk4/test.interval_list - md5sum: 67b15dff732693db3542e6b1dc30a5da - -- name: gatk4 filterintervals test_gatk4_filterintervals_stub - command: nextflow run ./tests/modules/nf-core/gatk4/filterintervals -entry test_gatk4_filterintervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filterintervals/nextflow.config -stub - tags: - - gatk4/filterintervals - - gatk4 - files: - - path: output/gatk4/test.interval_list diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf deleted file mode 100644 index 150c958c682..00000000000 --- a/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_GATHERBQSRREPORTS } from '../../../../../modules/nf-core/gatk4/gatherbqsrreports/main.nf' - -workflow test_gatk4_gatherbqsrreports { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true) - ] - - GATK4_GATHERBQSRREPORTS ( input ) -} - -workflow test_gatk4_gatherbqsrreports_multiple { - - input = [ - [ id:'test', single_end:false ], // meta map - [file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_baserecalibrator_table'], checkIfExists: true) - ] - ] - - GATK4_GATHERBQSRREPORTS ( input ) -} diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/nextflow.config b/tests/modules/nf-core/gatk4/gatherbqsrreports/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/gatk4/gatherbqsrreports/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/gatk4/gatherbqsrreports/test.yml b/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml deleted file mode 100644 index e70c49eaa86..00000000000 --- a/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports - command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports -c ./tests/config/nextflow.config - tags: - - gatk4 - - gatk4/gatherbqsrreports - files: - - path: output/gatk4/test.table - md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf - - path: output/gatk4/versions.yml - -- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple - command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c ./tests/config/nextflow.config - tags: - - gatk4 - - gatk4/gatherbqsrreports - files: - - path: output/gatk4/test.table - md5sum: 0c1257eececf95db8ca378272d0f21f9 - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf deleted file mode 100644 index a30364439f5..00000000000 --- a/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_GATHERPILEUPSUMMARIES } from '../../../../../modules/nf-core/gatk4/gatherpileupsummaries/main.nf' - -workflow test_gatk4_gatherpileupsummaries { - - input = [ - [ id:'test', single_end:false ], // meta map - [file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)] - //file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)] - ] - - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - - GATK4_GATHERPILEUPSUMMARIES ( input, dict ) -} diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/test.yml b/tests/modules/nf-core/gatk4/gatherpileupsummaries/test.yml deleted file mode 100644 index 835d20d2d7d..00000000000 --- a/tests/modules/nf-core/gatk4/gatherpileupsummaries/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: gatk4 gatherpileupsummaries - command: nextflow run ./tests/modules/nf-core/gatk4/gatherpileupsummaries -entry test_gatk4_gatherpileupsummaries -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config - tags: - - gatk4 - - gatk4/gatherpileupsummaries - files: - - path: output/gatk4/test.out.pileups.table - md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf deleted file mode 100644 index 5960a568964..00000000000 --- a/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../../modules/nf-core/gatk4/learnreadorientationmodel/main.nf' - -workflow test_gatk4_learnreadorientationmodel { - - input = [ [ id:'test' ], // meta map - [file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_f1r2_tar_gz'], checkIfExists: true)] ] - - GATK4_LEARNREADORIENTATIONMODEL ( input ) -} diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/test.yml b/tests/modules/nf-core/gatk4/learnreadorientationmodel/test.yml deleted file mode 100644 index fff1b387ac4..00000000000 --- a/tests/modules/nf-core/gatk4/learnreadorientationmodel/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: gatk4 learnreadorientationmodel test_gatk4_learnreadorientationmodel - command: nextflow run ./tests/modules/nf-core/gatk4/learnreadorientationmodel -entry test_gatk4_learnreadorientationmodel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config - tags: - - gatk4 - - gatk4/learnreadorientationmodel - files: - - path: output/gatk4/test.artifact-prior.tar.gz - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf deleted file mode 100644 index 8028168f366..00000000000 --- a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../../modules/nf-core/gatk4/leftalignandtrimvariants/main.nf' - -workflow test_gatk4_leftalignandtrimvariants_interval { - - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], 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) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - - GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict ) -} - -workflow test_gatk4_leftalignandtrimvariants_no_interval { - - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], 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) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - - GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict ) -} diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/test.yml b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/test.yml deleted file mode 100644 index 97afa0fa6f2..00000000000 --- a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/test.yml +++ /dev/null @@ -1,23 +0,0 @@ -- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_interval - command: nextflow run ./tests/modules/nf-core/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_interval -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config - tags: - - gatk4 - - gatk4/leftalignandtrimvariants - files: - - path: output/gatk4/test.normalised.vcf.gz - contains: - - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT" - - path: output/gatk4/test.normalised.vcf.gz.tbi - -- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_no_interval - command: nextflow run ./tests/modules/nf-core/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_no_interval -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config - tags: - - gatk4 - - gatk4/leftalignandtrimvariants - files: - - path: output/gatk4/test.normalised.vcf.gz - contains: - - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT" - - "MT192765.1\t10502\t.\tTAGATTATGACTGTGTCTCTTTTTGTTACATGCACCA\tTAGAT" - - path: output/gatk4/test.normalised.vcf.gz.tbi - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/mergebamalignment/main.nf b/tests/modules/nf-core/gatk4/mergebamalignment/main.nf deleted file mode 100644 index 90497e51b1a..00000000000 --- a/tests/modules/nf-core/gatk4/mergebamalignment/main.nf +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_MERGEBAMALIGNMENT } from '../../../../../modules/nf-core/gatk4/mergebamalignment/main.nf' - -workflow test_gatk4_mergebamalignment { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true) - ] - fasta = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - dict = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - ] - - GATK4_MERGEBAMALIGNMENT ( input, fasta, dict ) -} - -workflow test_gatk4_mergebamalignment_stubs { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true) - ] - fasta = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - dict = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - ] - - GATK4_MERGEBAMALIGNMENT ( input, fasta, dict ) -} diff --git a/tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config b/tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/gatk4/mergebamalignment/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/gatk4/mergebamalignment/test.yml b/tests/modules/nf-core/gatk4/mergebamalignment/test.yml deleted file mode 100644 index c918d6297c1..00000000000 --- a/tests/modules/nf-core/gatk4/mergebamalignment/test.yml +++ /dev/null @@ -1,18 +0,0 @@ -- name: gatk4 mergebamalignment test_gatk4_mergebamalignment - command: nextflow run ./tests/modules/nf-core/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config - tags: - - gatk4 - - gatk4/mergebamalignment - files: - - path: output/gatk4/test.bam - md5sum: e6f1b343700b7ccb94e81ae127433988 - - path: output/gatk4/versions.yml - -- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs - command: nextflow run ./tests/modules/nf-core/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config -stub-run - tags: - - gatk4 - - gatk4/mergebamalignment - files: - - path: output/gatk4/test.bam - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/preprocessintervals/main.nf b/tests/modules/nf-core/gatk4/preprocessintervals/main.nf deleted file mode 100644 index 4bebde64956..00000000000 --- a/tests/modules/nf-core/gatk4/preprocessintervals/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_PREPROCESSINTERVALS } from '../../../../../modules/nf-core/gatk4/preprocessintervals/main.nf' - -workflow test_gatk4_preprocessintervals { - - fasta = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - fai = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - dict = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - ] - exc_inter = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_blacklist_interval_bed'], checkIfExists: true) - ] - - GATK4_PREPROCESSINTERVALS ( fasta, fai, dict, [[],[]], exc_inter ) -} diff --git a/tests/modules/nf-core/gatk4/preprocessintervals/test.yml b/tests/modules/nf-core/gatk4/preprocessintervals/test.yml deleted file mode 100644 index 7fc0b075c47..00000000000 --- a/tests/modules/nf-core/gatk4/preprocessintervals/test.yml +++ /dev/null @@ -1,16 +0,0 @@ -- name: gatk4 preprocessintervals test_gatk4_preprocessintervals - command: nextflow run ./tests/modules/nf-core/gatk4/preprocessintervals -entry test_gatk4_preprocessintervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config - tags: - - gatk4/preprocessintervals - - gatk4 - files: - - path: output/gatk4/test.interval_list - md5sum: ce14b8fb47a60483fe44473ba40e1583 - -- name: gatk4 preprocessintervals test_gatk4_preprocessintervals_stub - command: nextflow run ./tests/modules/nf-core/gatk4/preprocessintervals -entry test_gatk4_preprocessintervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config -stub - tags: - - gatk4/preprocessintervals - - gatk4 - files: - - path: output/gatk4/test.interval_list diff --git a/tests/modules/nf-core/gatk4/printreads/main.nf b/tests/modules/nf-core/gatk4/printreads/main.nf deleted file mode 100644 index 4107651e8fc..00000000000 --- a/tests/modules/nf-core/gatk4/printreads/main.nf +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_PRINTREADS } from '../../../../../modules/nf-core/gatk4/printreads/main.nf' - -workflow test_gatk4_printreads_bam { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - - ] - - 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) - ] - dict = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - ] - - GATK4_PRINTREADS ( input, fasta, fai, dict ) -} - -workflow test_gatk4_printreads_cram { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) - - ] - - fasta = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - fai = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - dict = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - ] - - GATK4_PRINTREADS ( input, fasta, fai, dict ) -} diff --git a/tests/modules/nf-core/gatk4/printreads/nextflow.config b/tests/modules/nf-core/gatk4/printreads/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/gatk4/printreads/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/gatk4/printreads/test.yml b/tests/modules/nf-core/gatk4/printreads/test.yml deleted file mode 100644 index c42c20e58e7..00000000000 --- a/tests/modules/nf-core/gatk4/printreads/test.yml +++ /dev/null @@ -1,26 +0,0 @@ -- name: "gatk4 printreads bam" - command: nextflow run ./tests/modules/nf-core/gatk4/printreads -entry test_gatk4_printreads_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printreads/nextflow.config - tags: - - "gatk4" - - "gatk4/printreads" - files: - - path: "output/gatk4/test.bam" - - path: "output/gatk4/versions.yml" - -- name: "gatk4 printreads cram" - command: nextflow run ./tests/modules/nf-core/gatk4/printreads -entry test_gatk4_printreads_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printreads/nextflow.config - tags: - - "gatk4" - - "gatk4/printreads" - files: - - path: "output/gatk4/test.cram" - - path: "output/gatk4/versions.yml" - -- name: "gatk4 printreads stub" - command: nextflow run ./tests/modules/nf-core/gatk4/printreads -entry test_gatk4_printreads_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printreads/nextflow.config -stub - tags: - - "gatk4" - - "gatk4/printreads" - files: - - path: "output/gatk4/test.bam" - - path: "output/gatk4/versions.yml" diff --git a/tests/modules/nf-core/gatk4/revertsam/main.nf b/tests/modules/nf-core/gatk4/revertsam/main.nf deleted file mode 100644 index 2f4c153be69..00000000000 --- a/tests/modules/nf-core/gatk4/revertsam/main.nf +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_REVERTSAM } from '../../../../../modules/nf-core/gatk4/revertsam/main.nf' - -workflow test_gatk4_revertsam { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - GATK4_REVERTSAM ( input ) -} - -workflow test_gatk4_revertsam_stubs { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - GATK4_REVERTSAM ( input ) -} diff --git a/tests/modules/nf-core/gatk4/revertsam/nextflow.config b/tests/modules/nf-core/gatk4/revertsam/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/gatk4/revertsam/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/gatk4/revertsam/test.yml b/tests/modules/nf-core/gatk4/revertsam/test.yml deleted file mode 100644 index 9666fd19a40..00000000000 --- a/tests/modules/nf-core/gatk4/revertsam/test.yml +++ /dev/null @@ -1,18 +0,0 @@ -- name: gatk4 revertsam test_gatk4_revertsam - command: nextflow run ./tests/modules/nf-core/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/revertsam/nextflow.config - tags: - - gatk4 - - gatk4/revertsam - files: - - path: output/gatk4/test.reverted.bam - md5sum: f783a88deb45c3a2c20ca12cbe1c5652 - - path: output/gatk4/versions.yml - -- name: gatk4 revertsam test_gatk4_revertsam_stubs - command: nextflow run ./tests/modules/nf-core/gatk4/revertsam -entry test_gatk4_revertsam_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/revertsam/nextflow.config -stub-run - tags: - - gatk4 - - gatk4/revertsam - files: - - path: output/gatk4/test.reverted.bam - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/samtofastq/main.nf b/tests/modules/nf-core/gatk4/samtofastq/main.nf deleted file mode 100644 index 35f1f9d36c9..00000000000 --- a/tests/modules/nf-core/gatk4/samtofastq/main.nf +++ /dev/null @@ -1,29 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_SAMTOFASTQ } from '../../../../../modules/nf-core/gatk4/samtofastq/main.nf' - -workflow test_gatk4_samtofastq_single_end { - input = [ [ id:'test', single_end: true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ] - ] - - GATK4_SAMTOFASTQ ( input ) -} - -workflow test_gatk4_samtofastq_paired_end { - input = [ [ id:'test', single_end: false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] - ] - - GATK4_SAMTOFASTQ ( input ) -} - -workflow test_gatk4_samtofastq_paired_end_stubs { - input = [ [ id:'test', single_end: true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ] - ] - - GATK4_SAMTOFASTQ ( input ) -} diff --git a/tests/modules/nf-core/gatk4/samtofastq/nextflow.config b/tests/modules/nf-core/gatk4/samtofastq/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/gatk4/samtofastq/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/gatk4/samtofastq/test.yml b/tests/modules/nf-core/gatk4/samtofastq/test.yml deleted file mode 100644 index eb179abba4e..00000000000 --- a/tests/modules/nf-core/gatk4/samtofastq/test.yml +++ /dev/null @@ -1,31 +0,0 @@ -- name: gatk4 samtofastq test_gatk4_samtofastq_single_end - command: nextflow run ./tests/modules/nf-core/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/samtofastq/nextflow.config - tags: - - gatk4 - - gatk4/samtofastq - files: - - path: output/gatk4/test.fastq.gz - md5sum: 370979e8ecb385d0e91968c4124c08bd - - path: output/gatk4/versions.yml - -- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end - command: nextflow run ./tests/modules/nf-core/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/samtofastq/nextflow.config - tags: - - gatk4 - - gatk4/samtofastq - files: - - path: output/gatk4/test_1.fastq.gz - md5sum: 8b74ed77c5afdec6e10a0839931be7f4 - - path: output/gatk4/test_2.fastq.gz - md5sum: ec085c1af75d08205d209a6d6d5e0111 - - path: output/gatk4/versions.yml - -- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs - command: nextflow run ./tests/modules/nf-core/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/samtofastq/nextflow.config -stub-run - tags: - - gatk4 - - gatk4/samtofastq - files: - - path: output/gatk4/test_1.fastq.gz - - path: output/gatk4/test_2.fastq.gz - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/shiftfasta/main.nf b/tests/modules/nf-core/gatk4/shiftfasta/main.nf deleted file mode 100644 index 75e0e7f7879..00000000000 --- a/tests/modules/nf-core/gatk4/shiftfasta/main.nf +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_SHIFTFASTA } from '../../../../../modules/nf-core/gatk4/shiftfasta/main.nf' - -workflow test_gatk4_shiftfasta { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - index = [ - [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - dict = [ - [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - ] - - GATK4_SHIFTFASTA ( input, index, dict ) -} diff --git a/tests/modules/nf-core/gatk4/shiftfasta/test.yml b/tests/modules/nf-core/gatk4/shiftfasta/test.yml deleted file mode 100644 index 9d8c564fe7f..00000000000 --- a/tests/modules/nf-core/gatk4/shiftfasta/test.yml +++ /dev/null @@ -1,29 +0,0 @@ -- name: "gatk4 shiftfasta" - command: nextflow run ./tests/modules/nf-core/gatk4/shiftfasta -entry test_gatk4_shiftfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/shiftfasta/nextflow.config - tags: - - "gatk4" - - "gatk4/shiftfasta" - files: - - path: "output/gatk4/test_shift.back_chain" - - path: "output/gatk4/test_shift.dict" - - path: "output/gatk4/test_shift.fasta" - - path: "output/gatk4/test_shift.fasta.fai" - - path: "output/gatk4/test.intervals" - - path: "output/gatk4/test.shifted.intervals" - - path: "output/gatk4/test_shift.fasta.fai" - - path: "output/gatk4/versions.yml" - -- name: "gatk4 shiftfasta stub" - command: nextflow run ./tests/modules/nf-core/gatk4/shiftfasta -entry test_gatk4_shiftfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/shiftfasta/nextflow.config -stub - tags: - - "gatk4" - - "gatk4/shiftfasta" - files: - - path: "output/gatk4/test_shift.back_chain" - - path: "output/gatk4/test_shift.dict" - - path: "output/gatk4/test_shift.fasta" - - path: "output/gatk4/test_shift.fasta.fai" - - path: "output/gatk4/test.intervals" - - path: "output/gatk4/test.shifted.intervals" - - path: "output/gatk4/test_shift.fasta.fai" - - path: "output/gatk4/versions.yml" diff --git a/tests/modules/nf-core/gstama/collapse/main.nf b/tests/modules/nf-core/gstama/collapse/main.nf deleted file mode 100644 index 20c3ff74ccf..00000000000 --- a/tests/modules/nf-core/gstama/collapse/main.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GSTAMA_COLLAPSE } from '../../../../../modules/nf-core/gstama/collapse/main.nf' - -workflow test_gstama_collapse { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['aligned'], checkIfExists: true) - ] - genome = file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true) - - GSTAMA_COLLAPSE ( input, genome ) -} diff --git a/tests/modules/nf-core/gstama/collapse/test.yml b/tests/modules/nf-core/gstama/collapse/test.yml deleted file mode 100644 index 484fe1db4d9..00000000000 --- a/tests/modules/nf-core/gstama/collapse/test.yml +++ /dev/null @@ -1,24 +0,0 @@ -- name: gstama collapse test_gstama_collapse - command: nextflow run ./tests/modules/nf-core/gstama/collapse -entry test_gstama_collapse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gstama/collapse/nextflow.config - tags: - - gstama - - gstama/collapse - files: - - path: output/gstama/test_tc_collapsed.bed - md5sum: e5105198ed970a33ae0ecaa7bff421d9 - - path: output/gstama/test_tc_local_density_error.txt - md5sum: b917ac1f14eccd590b6881a686f324d5 - - path: output/gstama/test_tc_polya.txt - md5sum: 628ea62b918fc4f31e109f724d714a66 - - path: output/gstama/test_tc_read.txt - md5sum: d2685d7f24cd1611e0770a5ce25422fe - - path: output/gstama/test_tc_strand_check.txt - md5sum: 42cc52b2660b1e0b84e1c9ab37a965ec - - path: output/gstama/test_tc_trans_read.bed - md5sum: 0ca1a32f33ef05242d897d913802554b - - path: output/gstama/test_tc_trans_report.txt - md5sum: 33a86c15ca2acce36b2a5962f4c1adc4 - - path: output/gstama/test_tc_varcov.txt - md5sum: 587fd899ff658eb66b1770a35283bfcb - - path: output/gstama/test_tc_variants.txt - md5sum: 5b1165e9f33faba4f7207013fc27257e diff --git a/tests/modules/nf-core/gstama/merge/main.nf b/tests/modules/nf-core/gstama/merge/main.nf deleted file mode 100644 index dad081f557b..00000000000 --- a/tests/modules/nf-core/gstama/merge/main.nf +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GSTAMA_MERGE } from '../../../../../modules/nf-core/gstama/merge/main' - -workflow test_gstama_merge { - - input = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['homo_sapiens']['pacbio']['genemodel1'], checkIfExists: true), - file(params.test_data['homo_sapiens']['pacbio']['genemodel2'], checkIfExists: true) - ] - ] - filelist = file(params.test_data['homo_sapiens']['pacbio']['filelist'], checkIfExists: true) - - GSTAMA_MERGE ( input, filelist ) -} diff --git a/tests/modules/nf-core/gstama/merge/nextflow.config b/tests/modules/nf-core/gstama/merge/nextflow.config deleted file mode 100644 index e0d7c8ef185..00000000000 --- a/tests/modules/nf-core/gstama/merge/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GSTAMA_MERGE { - ext.prefix = { "${meta.id}_merged" } - } - -} diff --git a/tests/modules/nf-core/gstama/merge/test.yml b/tests/modules/nf-core/gstama/merge/test.yml deleted file mode 100644 index b0a81a3f1bc..00000000000 --- a/tests/modules/nf-core/gstama/merge/test.yml +++ /dev/null @@ -1,14 +0,0 @@ -- name: gstama merge test_gstama_merge - command: nextflow run ./tests/modules/nf-core/gstama/merge -entry test_gstama_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gstama/merge/nextflow.config - tags: - - gstama - - gstama/merge - files: - - path: output/gstama/test_merged.bed - md5sum: 60ec34e1ff9655d4ce2e83d3f4bbf448 - - path: output/gstama/test_merged_gene_report.txt - md5sum: 7029fd183dfd905a233403cfbe44722a - - path: output/gstama/test_merged_merge.txt - md5sum: 4279e59ed5739ce4f2f811568962893f - - path: output/gstama/test_merged_trans_report.txt - md5sum: 97d8346d9eb9da140941656c3a3325cd diff --git a/tests/modules/nf-core/gstama/polyacleanup/main.nf b/tests/modules/nf-core/gstama/polyacleanup/main.nf deleted file mode 100644 index e1ed59663f9..00000000000 --- a/tests/modules/nf-core/gstama/polyacleanup/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GSTAMA_POLYACLEANUP } from '../../../../../modules/nf-core/gstama/polyacleanup/main.nf' - -workflow test_gstama_polyacleanup { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true) - ] - - GSTAMA_POLYACLEANUP ( input ) -} diff --git a/tests/modules/nf-core/gstama/polyacleanup/nextflow.config b/tests/modules/nf-core/gstama/polyacleanup/nextflow.config deleted file mode 100644 index ff4077028bf..00000000000 --- a/tests/modules/nf-core/gstama/polyacleanup/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.prefix = { "${meta.id}_tama" } - -} diff --git a/tests/modules/nf-core/gstama/polyacleanup/test.yml b/tests/modules/nf-core/gstama/polyacleanup/test.yml deleted file mode 100644 index 6a1ed064c0e..00000000000 --- a/tests/modules/nf-core/gstama/polyacleanup/test.yml +++ /dev/null @@ -1,14 +0,0 @@ -- name: gstama polyacleanup test_gstama_polyacleanup - command: nextflow run ./tests/modules/nf-core/gstama/polyacleanup -entry test_gstama_polyacleanup -c ./tests/config/nextflow.config - tags: - - gstama - - gstama/polyacleanup - files: - - path: output/gstama/test_tama.fa.gz - md5sum: 9c768387478e5f966a42c369c0270b09 - - path: output/gstama/test_tama_polya_flnc_report.txt.gz - md5sum: fe3606979ed11538aacd83159f4cff03 - - path: output/gstama/test_tama_tails.fa.gz - md5sum: ba21256c0afe0bda71b3ee66b4c761bf - - path: output/gstama/versions.yml - md5sum: 07ebb812ae13a350d955fab7600b2542 diff --git a/tests/modules/nf-core/happy/sompy/main.nf b/tests/modules/nf-core/happy/sompy/main.nf deleted file mode 100644 index bec0ada84ba..00000000000 --- a/tests/modules/nf-core/happy/sompy/main.nf +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HAPPY_SOMPY } from '../../../../../modules/nf-core/happy/sompy/main.nf' - -workflow test_sompy { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), - [], - [] - ] - - fasta = [ - [ id:'test1' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - fasta_fai = [ - [ id:'test1' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - - HAPPY_SOMPY ( - input, - fasta, - fasta_fai, - [[],[]], - [[],[]], - [[],[]] - ) -} -workflow test_sompy_bam { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), - [], - [] - ] - - fasta = [ - [ id:'test1' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - fasta_fai = [ - [ id:'test1' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - - bam = [ - [id:'test2'], - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists:true) - ] - - HAPPY_SOMPY ( - input, - fasta, - fasta_fai, - [[],[]], - [[],[]], - bam - ) -} diff --git a/tests/modules/nf-core/happy/sompy/nextflow.config b/tests/modules/nf-core/happy/sompy/nextflow.config deleted file mode 100644 index 32d6b83227b..00000000000 --- a/tests/modules/nf-core/happy/sompy/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: HAPPY_SOMPY { - ext.args = '--feature-table hcc.mutect.snv' - } -} diff --git a/tests/modules/nf-core/happy/sompy/test.yml b/tests/modules/nf-core/happy/sompy/test.yml deleted file mode 100644 index 6bde5712fb9..00000000000 --- a/tests/modules/nf-core/happy/sompy/test.yml +++ /dev/null @@ -1,25 +0,0 @@ -- name: happy sompy test_sompy - command: nextflow run ./tests/modules/nf-core/happy/sompy -entry test_sompy -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/happy/sompy/nextflow.config - tags: - - happy - - happy/sompy - files: - - path: output/happy/test.features.csv - md5sum: 34a8239e739edd5ea89be78b86262d4e - - path: output/happy/test.metrics.json - - path: output/happy/test.stats.csv - md5sum: 402dc827ee8ec5e155fc7ea47232963e - - path: output/happy/versions.yml - -- name: happy sompy test_sompy_bam - command: nextflow run ./tests/modules/nf-core/happy/sompy -entry test_sompy_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/happy/sompy/nextflow.config - tags: - - happy - - happy/sompy - files: - - path: output/happy/test.features.csv - md5sum: 34a8239e739edd5ea89be78b86262d4e - - path: output/happy/test.metrics.json - - path: output/happy/test.stats.csv - md5sum: 72653d4fa9150f54395c37e2220b2468 - - path: output/happy/versions.yml diff --git a/tests/modules/nf-core/picard/bedtointervallist/main.nf b/tests/modules/nf-core/picard/bedtointervallist/main.nf deleted file mode 100644 index 55a40a25ab7..00000000000 --- a/tests/modules/nf-core/picard/bedtointervallist/main.nf +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/picard/bedtointervallist/main.nf' - -workflow test_picard_bedtointervallist { - input = [ - [ id:'test' ], // meta map - [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] - ] - dict = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - ] - - PICARD_BEDTOINTERVALLIST ( input, dict, [] ) -} diff --git a/tests/modules/nf-core/picard/bedtointervallist/nextflow.config b/tests/modules/nf-core/picard/bedtointervallist/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/picard/bedtointervallist/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/picard/bedtointervallist/test.yml b/tests/modules/nf-core/picard/bedtointervallist/test.yml deleted file mode 100644 index 51c9dfba79f..00000000000 --- a/tests/modules/nf-core/picard/bedtointervallist/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: picard bedtointervallist test_picard_bedtointervallist - command: nextflow run ./tests/modules/nf-core/picard/bedtointervallist -entry test_picard_bedtointervallist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/bedtointervallist/nextflow.config - tags: - - picard/bedtointervallist - - picard - files: - - path: output/picard/test.interval_list - md5sum: e51101c9357fb2d59fd30e370eefa39c diff --git a/tests/modules/nf-core/picard/cleansam/main.nf b/tests/modules/nf-core/picard/cleansam/main.nf deleted file mode 100644 index d337aca51ee..00000000000 --- a/tests/modules/nf-core/picard/cleansam/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_CLEANSAM } from '../../../../../modules/nf-core/picard/cleansam/main.nf' - -workflow test_picard_cleansam { - - input = [ - [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) - ] - - PICARD_CLEANSAM ( input ) -} diff --git a/tests/modules/nf-core/picard/cleansam/test.yml b/tests/modules/nf-core/picard/cleansam/test.yml deleted file mode 100644 index fd80f244cae..00000000000 --- a/tests/modules/nf-core/picard/cleansam/test.yml +++ /dev/null @@ -1,18 +0,0 @@ -- name: picard cleansam test_picard_cleansam - command: nextflow run ./tests/modules/nf-core/picard/cleansam -entry test_picard_cleansam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/cleansam/nextflow.config - tags: - - picard/cleansam - - picard - files: - - path: output/picard/test.cleaned.bam - md5sum: a48f8e77a1480445efc57570c3a38a68 - - path: output/picard/versions.yml - -- name: picard cleansam test_picard_cleansam stub - command: nextflow run ./tests/modules/nf-core/picard/cleansam -entry test_picard_cleansam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/cleansam/nextflow.config -stub-run - tags: - - picard/cleansam - - picard - files: - - path: output/picard/test.cleaned.bam - - path: output/picard/versions.yml diff --git a/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf b/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf deleted file mode 100644 index 12ea0022356..00000000000 --- a/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ /dev/null @@ -1,48 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../../modules/nf-core/picard/collectmultiplemetrics/main.nf' - -workflow test_picard_collectmultiplemetrics { - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ] - fasta = [ - [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - fai = [[id:'genome'],[]] - - PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, fai ) -} - -workflow test_picard_collectmultiplemetrics_nofasta { - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ] - - PICARD_COLLECTMULTIPLEMETRICS ( input, [[id:'genome'],[]], [[id:'genome'],[]] ) -} - -workflow test_picard_collectmultiplemetrics_cram { - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ] - fasta = [ - [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - fai = [ - [id:'genome'], - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - - PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, fai ) -} diff --git a/tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config b/tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/picard/collectmultiplemetrics/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/picard/collectmultiplemetrics/test.yml b/tests/modules/nf-core/picard/collectmultiplemetrics/test.yml deleted file mode 100644 index c8e987d9d28..00000000000 --- a/tests/modules/nf-core/picard/collectmultiplemetrics/test.yml +++ /dev/null @@ -1,93 +0,0 @@ -- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics - command: nextflow run ./tests/modules/nf-core/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config - tags: - - picard/collectmultiplemetrics - - picard - files: - - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics - contains: - - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics" - - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf - - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics - contains: - - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N" - - "1\t1\t20\t26\t32\t22\t0" - - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf - - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics - contains: - - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP" - - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311" - - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf - - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics - contains: - - "CYCLE\tMEAN_QUALITY" - - "1\t32" - - "2\t31.35" - - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf - - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics - contains: - - "QUALITY\tCOUNT_OF_Q" - - "14\t1926" - - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf - - path: output/picard/versions.yml - -- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta - command: nextflow run ./tests/modules/nf-core/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config - tags: - - picard/collectmultiplemetrics - - picard - files: - - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics - contains: - - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics" - - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf - - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics - contains: - - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N" - - "1\t1\t20\t26\t32\t22\t0" - - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf - - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics - contains: - - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP" - - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311" - - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf - - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics - contains: - - "CYCLE\tMEAN_QUALITY" - - "1\t32" - - "2\t31.35" - - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf - - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics - contains: - - "QUALITY\tCOUNT_OF_Q" - - "14\t1926" - - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf - - path: output/picard/versions.yml - -- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_cram - command: nextflow run ./tests/modules/nf-core/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config - tags: - - picard/collectmultiplemetrics - - picard - files: - - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics - contains: - - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics" - - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf - - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics - contains: - - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N" - - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf - - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics - contains: - - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP" - - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf - - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics - contains: - - "CYCLE\tMEAN_QUALITY" - - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf - - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics - contains: - - "QUALITY\tCOUNT_OF_Q" - - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf - - path: output/picard/versions.yml diff --git a/tests/modules/nf-core/picard/fastqtosam/main.nf b/tests/modules/nf-core/picard/fastqtosam/main.nf deleted file mode 100644 index 5b1af7ea9fc..00000000000 --- a/tests/modules/nf-core/picard/fastqtosam/main.nf +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_FASTQTOSAM } from '../../../../../modules/nf-core/picard/fastqtosam/main.nf' - -workflow test_picard_fastqtosam_single { - - input = [ - [ id:'test', single_end:true ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] - - PICARD_FASTQTOSAM ( input ) -} - -workflow test_picard_fastqtosam_paired { - - input = [ - [ 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) - ] - ] - - PICARD_FASTQTOSAM ( input ) -} - -workflow test_picard_fastqtosam_paired_custom_samplename { - - input = [ - [ 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) - ] - ] - - PICARD_FASTQTOSAM ( input ) -} diff --git a/tests/modules/nf-core/picard/fastqtosam/nextflow.config b/tests/modules/nf-core/picard/fastqtosam/nextflow.config deleted file mode 100644 index 25c849c9e85..00000000000 --- a/tests/modules/nf-core/picard/fastqtosam/nextflow.config +++ /dev/null @@ -1,7 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: "test_picard_fastqtosam_paired_custom_samplename:PICARD_FASTQTOSAM" { - ext.args = "--SAMPLE_NAME CustomSample" - } -} diff --git a/tests/modules/nf-core/picard/fastqtosam/test.yml b/tests/modules/nf-core/picard/fastqtosam/test.yml deleted file mode 100644 index 348337c46b9..00000000000 --- a/tests/modules/nf-core/picard/fastqtosam/test.yml +++ /dev/null @@ -1,26 +0,0 @@ -- name: picard fastqtosam test_picard_fastqtosam_single - command: nextflow run ./tests/modules/nf-core/picard/fastqtosam -entry test_picard_fastqtosam_single -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fastqtosam/nextflow.config - tags: - - picard - - picard/fastqtosam - files: - - path: output/picard/test.bam - md5sum: fe2882efe8f13a8da20fcc63469ed0aa - -- name: picard fastqtosam test_picard_fastqtosam_paired - command: nextflow run ./tests/modules/nf-core/picard/fastqtosam -entry test_picard_fastqtosam_paired -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fastqtosam/nextflow.config - tags: - - picard - - picard/fastqtosam - files: - - path: output/picard/test.bam - md5sum: 90e4f59f9d942f96c3f3c41160f3fd5d - -- name: picard fastqtosam test_picard_fastqtosam_paired_custom_samplename - command: nextflow run ./tests/modules/nf-core/picard/fastqtosam -entry test_picard_fastqtosam_paired_custom_samplename -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fastqtosam/nextflow.config - tags: - - picard - - picard/fastqtosam - files: - - path: output/picard/test.bam - md5sum: 69d35ee2b5dc263d022eaf59a9e383d3 diff --git a/tests/modules/nf-core/picard/fixmateinformation/main.nf b/tests/modules/nf-core/picard/fixmateinformation/main.nf deleted file mode 100644 index 92277611f29..00000000000 --- a/tests/modules/nf-core/picard/fixmateinformation/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_FIXMATEINFORMATION } from '../../../../../modules/nf-core/picard/fixmateinformation/main.nf' - -workflow test_picard_fixmateinformation { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - PICARD_FIXMATEINFORMATION ( input ) -} diff --git a/tests/modules/nf-core/picard/fixmateinformation/nextflow.config b/tests/modules/nf-core/picard/fixmateinformation/nextflow.config deleted file mode 100644 index 431e8c71024..00000000000 --- a/tests/modules/nf-core/picard/fixmateinformation/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - - withName: PICARD_FIXMATEINFORMATION { - ext.prefix = { "${meta.id}.fixed" } - } -} diff --git a/tests/modules/nf-core/picard/fixmateinformation/test.yml b/tests/modules/nf-core/picard/fixmateinformation/test.yml deleted file mode 100644 index e62e9250b28..00000000000 --- a/tests/modules/nf-core/picard/fixmateinformation/test.yml +++ /dev/null @@ -1,18 +0,0 @@ -- name: picard fixmateinformation test_picard_fixmateinformation - command: nextflow run ./tests/modules/nf-core/picard/fixmateinformation -entry test_picard_fixmateinformation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fixmateinformation/nextflow.config - tags: - - picard/fixmateinformation - - picard - files: - - path: output/picard/test.fixed.bam - md5sum: 746102e8c242c0ef42e045c49d320030 - - path: output/picard/versions.yml - -- name: picard fixmateinformation test_picard_fixmateinformation stub - command: nextflow run ./tests/modules/nf-core/picard/fixmateinformation -entry test_picard_fixmateinformation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fixmateinformation/nextflow.config -stub-run - tags: - - picard/fixmateinformation - - picard - files: - - path: output/picard/test.fixed.bam - - path: output/picard/versions.yml diff --git a/tests/modules/nf-core/picard/liftovervcf/main.nf b/tests/modules/nf-core/picard/liftovervcf/main.nf deleted file mode 100644 index 1cecc56e643..00000000000 --- a/tests/modules/nf-core/picard/liftovervcf/main.nf +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_LIFTOVERVCF } from '../../../../../modules/nf-core/picard/liftovervcf/main.nf' - -workflow test_picard_liftovervcf { - - input_vcf = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) - ] - dict = [ [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - ] - chain = [ [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true) - ] - fasta = [ [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - PICARD_LIFTOVERVCF ( input_vcf, dict, fasta, chain ) -} - -workflow test_picard_liftovervcf_stubs { - - input_vcf = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) - ] - dict = [ [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - ] - chain = [ [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true) - ] - fasta = [ [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - - PICARD_LIFTOVERVCF ( input_vcf, dict, fasta, chain ) -} diff --git a/tests/modules/nf-core/picard/liftovervcf/nextflow.config b/tests/modules/nf-core/picard/liftovervcf/nextflow.config deleted file mode 100644 index f69fc351ad6..00000000000 --- a/tests/modules/nf-core/picard/liftovervcf/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - ext.args = "--WARN_ON_MISSING_CONTIG true" - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/picard/liftovervcf/test.yml b/tests/modules/nf-core/picard/liftovervcf/test.yml deleted file mode 100644 index 09bd2dd14c2..00000000000 --- a/tests/modules/nf-core/picard/liftovervcf/test.yml +++ /dev/null @@ -1,21 +0,0 @@ -- name: picard liftovervcf test_picard_liftovervcf - command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf -c ./tests/config/nextflow.config - tags: - - picard/liftovervcf - - picard - files: - - path: output/picard/test.lifted.vcf.gz - contains: - - "chr22" - - path: output/picard/test.unlifted.vcf.gz - - path: output/picard/versions.yml - -- name: picard liftovervcf test_picard_liftovervcf_stubs - command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf_stubs -c ./tests/config/nextflow.config -stub-run - tags: - - picard/liftovervcf - - picard - files: - - path: output/picard/test.lifted.vcf.gz - - path: output/picard/test.unlifted.vcf.gz - - path: output/picard/versions.yml diff --git a/tests/modules/nf-core/picard/renamesampleinvcf/main.nf b/tests/modules/nf-core/picard/renamesampleinvcf/main.nf deleted file mode 100644 index a17975be5fb..00000000000 --- a/tests/modules/nf-core/picard/renamesampleinvcf/main.nf +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_RENAMESAMPLEINVCF } from '../../../../../modules/nf-core/picard/renamesampleinvcf/main.nf' - -workflow test_picard_renamesampleinvcf { - - input = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) - ] - - PICARD_RENAMESAMPLEINVCF ( input ) -} diff --git a/tests/modules/nf-core/picard/renamesampleinvcf/nextflow.config b/tests/modules/nf-core/picard/renamesampleinvcf/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/picard/renamesampleinvcf/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/picard/renamesampleinvcf/test.yml b/tests/modules/nf-core/picard/renamesampleinvcf/test.yml deleted file mode 100644 index 3b2f8e06299..00000000000 --- a/tests/modules/nf-core/picard/renamesampleinvcf/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: picard renamesampleinvcf test_picard_renamesampleinvcf - command: nextflow run ./tests/modules/nf-core/picard/renamesampleinvcf -entry test_picard_renamesampleinvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/renamesampleinvcf/nextflow.config - tags: - - picard - - picard/renamesampleinvcf - files: - - path: output/picard/test_renam.vcf.gz - md5sum: 6664b59319777b3152fcccc79c35fdb8 - - path: output/picard/versions.yml - -- name: picard renamesampleinvcf test_picard_renamesampleinvcf_stub - command: nextflow run ./tests/modules/nf-core/picard/renamesampleinvcf -entry test_picard_renamesampleinvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/renamesampleinvcf/nextflow.config -stub-run - tags: - - picard - - picard/renamesampleinvcf - files: - - path: output/picard/test_renam.vcf.gz diff --git a/tests/modules/nf-core/picard/sortsam/main.nf b/tests/modules/nf-core/picard/sortsam/main.nf deleted file mode 100644 index 4b4e801355a..00000000000 --- a/tests/modules/nf-core/picard/sortsam/main.nf +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_SORTSAM } from '../../../../../modules/nf-core/picard/sortsam/main.nf' - -workflow test_picard_sortsam { - - input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ] - sort_order = "queryname" - - PICARD_SORTSAM ( input, sort_order ) -} diff --git a/tests/modules/nf-core/picard/sortsam/nextflow.config b/tests/modules/nf-core/picard/sortsam/nextflow.config deleted file mode 100644 index ca572c2f41c..00000000000 --- a/tests/modules/nf-core/picard/sortsam/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: PICARD_SORTSAM { - ext.prefix = { "${meta.id}.sorted" } - } - -} diff --git a/tests/modules/nf-core/picard/sortsam/test.yml b/tests/modules/nf-core/picard/sortsam/test.yml deleted file mode 100644 index 9322ed77b5b..00000000000 --- a/tests/modules/nf-core/picard/sortsam/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: picard sortsam test_picard_sortsam - command: nextflow run ./tests/modules/nf-core/picard/sortsam -entry test_picard_sortsam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/sortsam/nextflow.config - tags: - - picard - - picard/sortsam - files: - - path: output/picard/test.sorted.bam - md5sum: b44a6ca04811a9470c7813c3c9465fd5 - - path: output/picard/versions.yml diff --git a/tests/modules/nf-core/picard/sortvcf/main.nf b/tests/modules/nf-core/picard/sortvcf/main.nf deleted file mode 100644 index c374b5b575c..00000000000 --- a/tests/modules/nf-core/picard/sortvcf/main.nf +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_SORTVCF } from '../../../../../modules/nf-core/picard/sortvcf/main.nf' - -workflow test_picard_sortvcf { - - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) - ] - - fasta = [ [ id:'genome' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - dict = [ [ id:'genome' ], - file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - ] - - PICARD_SORTVCF ( input, fasta, dict ) -} diff --git a/tests/modules/nf-core/picard/sortvcf/nextflow.config b/tests/modules/nf-core/picard/sortvcf/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/picard/sortvcf/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/picard/sortvcf/test.yml b/tests/modules/nf-core/picard/sortvcf/test.yml deleted file mode 100644 index 67458bdf65a..00000000000 --- a/tests/modules/nf-core/picard/sortvcf/test.yml +++ /dev/null @@ -1,7 +0,0 @@ -- name: picard sortvcf - command: nextflow run ./tests/modules/nf-core/picard/sortvcf -entry test_picard_sortvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/sortvcf/nextflow.config - tags: - - picard - - picard/sortvcf - files: - - path: output/picard/test_sorted.vcf.gz