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/atlas/call/meta.yml b/modules/nf-core/atlas/call/meta.yml index 9b1142bdd94..a07bc6a7dd7 100644 --- a/modules/nf-core/atlas/call/meta.yml +++ b/modules/nf-core/atlas/call/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" doi: "10.1101/105346" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map @@ -48,7 +48,7 @@ input: description: Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation. pattern: "*.{txt.tsv}" - method: - type: character + type: string description: Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation. pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase" output: @@ -61,7 +61,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - - bam: + - vcf: type: file description: VCF file with variant calls pattern: "*.vcf.gz" diff --git a/modules/nf-core/atlas/call/tests/main.nf.test b/modules/nf-core/atlas/call/tests/main.nf.test new file mode 100644 index 00000000000..dbd40640873 --- /dev/null +++ b/modules/nf-core/atlas/call/tests/main.nf.test @@ -0,0 +1,46 @@ + +nextflow_process { + + name "Test Process ATLAS_CALL" + script "../main.nf" + process "ATLAS_CALL" + + tag "modules" + tag "modules_nfcore" + tag "atlas" + tag "atlas/call" + + test("test-atlas-call") { + + 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] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = [] + input[4] = 'randomBase' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.summary, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/atlas/call/tests/main.nf.test.snap b/modules/nf-core/atlas/call/tests/main.nf.test.snap new file mode 100644 index 00000000000..c5a406b2227 --- /dev/null +++ b/modules/nf-core/atlas/call/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-atlas-call": { + "content": [ + "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=12674, phased=true, phasedAutodetect=true]", + [ + "versions.yml:md5,abad4c906071792f8a5270fdb143fc4e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T15:48:22.930389" + } +} \ No newline at end of file diff --git a/modules/nf-core/atlas/pmd/meta.yml b/modules/nf-core/atlas/pmd/meta.yml index 7b11d718e48..ed2ec3691ba 100644 --- a/modules/nf-core/atlas/pmd/meta.yml +++ b/modules/nf-core/atlas/pmd/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" doi: "10.1101/105346" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/atlas/pmd/tests/main.nf.test b/modules/nf-core/atlas/pmd/tests/main.nf.test new file mode 100644 index 00000000000..fc804e7b170 --- /dev/null +++ b/modules/nf-core/atlas/pmd/tests/main.nf.test @@ -0,0 +1,46 @@ + +nextflow_process { + + name "Test Process ATLAS_PMD" + script "../main.nf" + process "ATLAS_PMD" + + tag "modules" + tag "modules_nfcore" + tag "atlas" + tag "atlas/pmd" + + test("test-atlas-pmd") { + + 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) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.empiric[0][1]).readLines()[0], + file(process.out.exponential[0][1]).readLines()[0][0..13], + file(process.out.counts[0][1]).readLines()[0], + file(process.out.table[0][1]).readLines()[0], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/atlas/pmd/tests/main.nf.test.snap b/modules/nf-core/atlas/pmd/tests/main.nf.test.snap new file mode 100644 index 00000000000..59f90a820f7 --- /dev/null +++ b/modules/nf-core/atlas/pmd/tests/main.nf.test.snap @@ -0,0 +1,18 @@ +{ + "test-atlas-pmd": { + "content": [ + "1\tCT\tEmpiric[0.000831,0.000000,0.001339,0.001350,0.001437,0.000000,0.002210,0.001314,0.001466,0.000000,0.001395,0.001403,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.001362,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000794,0.000000,0.000000,0.000000,0.001297,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000]", + "1\tExponential[", + "1\tforward\tA->A\t2050\t2033\t2081\t2078\t2138\t2119\t2038\t2007\t2035\t2113\t2049\t2048\t1974\t2012\t2066\t2093\t2110\t1971\t1976\t1906\t1968\t1951\t1917\t1912\t1955\t1956\t1933\t1872\t1922\t1933\t1974\t1840\t1963\t1897\t1870\t1823\t1923\t1908\t1902\t1883\t1973\t1899\t1908\t1912\t1972\t1913\t1922\t1959\t1995\t2039", + "1\tforward\tA->A\t0.998539\t0.997547\t0.997603\t1\t0.998133\t0.998586\t0.99902\t0.998507\t0.998038\t0.999527\t0.997566\t0.997565\t0.998988\t0.998016\t0.99855\t0.999522\t0.996223\t0.99848\t0.999494\t0.998952\t0.999492\t0.997444\t0.998958\t0.997912\t0.997958\t0.997959\t0.997935\t0.998933\t0.996888\t0.999483\t0.998988\t0.999457\t0.998474\t0.998947\t0.998398\t0.998357\t0.997924\t0.999476\t0.999475\t1\t0.998987\t0.998423\t0.999476\t1\t1\t0.998956\t0.998442\t0.997454\t0.9975\t0.99951", + [ + "versions.yml:md5,abec49256c52cb677fa0dad3473ed5a6" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T16:01:09.837624" + } +} \ No newline at end of file diff --git a/modules/nf-core/atlas/recal/meta.yml b/modules/nf-core/atlas/recal/meta.yml index 886e93cb4e6..47b9c9afe6d 100644 --- a/modules/nf-core/atlas/recal/meta.yml +++ b/modules/nf-core/atlas/recal/meta.yml @@ -1,15 +1,16 @@ name: "atlas_recal" -description: gives an estimation of the sequencing bias based on known invariant sites +description: Gives an estimation of the sequencing bias based on known invariant sites keywords: - sequencing_bias - ATLAS + - bias tools: - "atlas": description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" doi: "10.1101/105346" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/atlas/recal/tests/main.nf.test b/modules/nf-core/atlas/recal/tests/main.nf.test new file mode 100644 index 00000000000..e03c6208b36 --- /dev/null +++ b/modules/nf-core/atlas/recal/tests/main.nf.test @@ -0,0 +1,44 @@ + +nextflow_process { + + name "Test Process ATLAS_RECAL" + script "../main.nf" + process "ATLAS_RECAL" + + tag "modules" + tag "modules_nfcore" + tag "atlas" + tag "atlas/recal" + + test("test-atlas-recal") { + + 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] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.recal_patterns[0][1]).readLines()[0], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/atlas/recal/tests/main.nf.test.snap b/modules/nf-core/atlas/recal/tests/main.nf.test.snap new file mode 100644 index 00000000000..a780f7c9b17 --- /dev/null +++ b/modules/nf-core/atlas/recal/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-atlas-recal": { + "content": [ + "readGroup\tmate\tmodel\tquality\tposition\tcontext", + [ + "versions.yml:md5,69864cf23ffc5b0559af20e0675c4290" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T15:57:16.06295" + } +} \ No newline at end of file diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index 1a4725cf1ec..222b55af7eb 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -11,7 +11,8 @@ process ATLAS_SPLITMERGE { tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist) output: - tuple val(meta), path("*_mergedReads.bam"), path("*.txt.gz"), emit: data + tuple val(meta), path("*_mergedReads.bam") , emit: bam + tuple val(meta), path("*.txt.gz") , emit: txt path "versions.yml", emit: versions when: diff --git a/modules/nf-core/atlas/splitmerge/meta.yml b/modules/nf-core/atlas/splitmerge/meta.yml index fc6289c78da..24621b1901b 100644 --- a/modules/nf-core/atlas/splitmerge/meta.yml +++ b/modules/nf-core/atlas/splitmerge/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" doi: "10.1101/105346" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map @@ -27,7 +27,7 @@ input: type: file description: The BAI file for the input BAM file pattern: "*.bai" - - read_group_setting: + - read_group_settings: type: file description: | TXT file containing the split and merge settings for @@ -55,7 +55,7 @@ output: type: file description: A BAM file with suffix_mergedReads.bam pattern: "*_mergedReads.bam" - - filelist: + - txt: type: file description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz pattern: "*.txt.gz" diff --git a/modules/nf-core/atlas/splitmerge/tests/main.nf.test b/modules/nf-core/atlas/splitmerge/tests/main.nf.test new file mode 100644 index 00000000000..9d7d1884b97 --- /dev/null +++ b/modules/nf-core/atlas/splitmerge/tests/main.nf.test @@ -0,0 +1,43 @@ + +nextflow_process { + + name "Test Process ATLAS_SPLITMERGE" + script "../main.nf" + process "ATLAS_SPLITMERGE" + + tag "modules" + tag "modules_nfcore" + tag "atlas" + tag "atlas/splitmerge" + + test("test-atlas-splitmerge") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + 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/bam/read_group_settings.txt', checkIfExists: true), + [] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.txt[0][1]).linesGzip[3..7], + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/atlas/splitmerge/tests/main.nf.test.snap b/modules/nf-core/atlas/splitmerge/tests/main.nf.test.snap new file mode 100644 index 00000000000..dfb38da0af1 --- /dev/null +++ b/modules/nf-core/atlas/splitmerge/tests/main.nf.test.snap @@ -0,0 +1,22 @@ +{ + "test-atlas-splitmerge": { + "content": [ + [ + "Read testN:1, rev : not a proper pair (orphan)", + "Read testN:99, rev : longer than insert size (TLEN)", + "Read testN:99, rev : not a proper pair (orphan)", + "Read testN:830, rev : longer than insert size (TLEN)", + "Read testN:830, fwd : longer than insert size (TLEN)" + ], + "66f5f17da47cc4dced99bd17d739b536", + [ + "versions.yml:md5,208f6ef7923cec00ddbcd5825f84a4fa" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T15:33:41.150912" + } +} \ No newline at end of file diff --git a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test new file mode 100644 index 00000000000..0d4f80ae699 --- /dev/null +++ b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test @@ -0,0 +1,37 @@ + +nextflow_process { + + name "Test Process BAM2FASTX_BAM2FASTQ" + script "../main.nf" + process "BAM2FASTX_BAM2FASTQ" + + tag "modules" + tag "modules_nfcore" + tag "bam2fastx" + tag "bam2fastx/bam2fastq" + + test("test-bam2fastx-bam2fastq") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam.pbi', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + } + +} diff --git a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap new file mode 100644 index 00000000000..342241ef940 --- /dev/null +++ b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test-bam2fastx-bam2fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1" + ] + ], + "1": [ + "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb" + ], + "fastq": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1" + ] + ], + "versions": [ + "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T06:30:10.25178642" + } +} \ No newline at end of file diff --git a/modules/nf-core/bamtools/stats/tests/main.nf.test b/modules/nf-core/bamtools/stats/tests/main.nf.test new file mode 100644 index 00000000000..478a6f0e84d --- /dev/null +++ b/modules/nf-core/bamtools/stats/tests/main.nf.test @@ -0,0 +1,35 @@ + +nextflow_process { + + name "Test Process BAMTOOLS_STATS" + script "../main.nf" + process "BAMTOOLS_STATS" + + tag "modules" + tag "modules_nfcore" + tag "bamtools" + tag "bamtools/stats" + + test("test-bamtools-stats") { + + 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/bamtools/stats/tests/main.nf.test.snap b/modules/nf-core/bamtools/stats/tests/main.nf.test.snap new file mode 100644 index 00000000000..c12ce29e5fb --- /dev/null +++ b/modules/nf-core/bamtools/stats/tests/main.nf.test.snap @@ -0,0 +1,37 @@ +{ + "test-bamtools-stats": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.stats:md5,b7c3f01682673a652d664a2889b15b66" + ] + ], + "1": [ + "versions.yml:md5,cdecc135c35467721cc72a58b542323b" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.stats:md5,b7c3f01682673a652d664a2889b15b66" + ] + ], + "versions": [ + "versions.yml:md5,cdecc135c35467721cc72a58b542323b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T15:23:51.167984" + } +} \ No newline at end of file diff --git a/modules/nf-core/bamutil/trimbam/tests/main.nf.test b/modules/nf-core/bamutil/trimbam/tests/main.nf.test new file mode 100644 index 00000000000..6ce0bbdd2aa --- /dev/null +++ b/modules/nf-core/bamutil/trimbam/tests/main.nf.test @@ -0,0 +1,41 @@ + +nextflow_process { + + name "Test Process BAMUTIL_TRIMBAM" + script "../main.nf" + process "BAMUTIL_TRIMBAM" + + tag "modules" + tag "modules_nfcore" + tag "bamutil" + tag "bamutil/trimbam" + + test("test-bamutil-trimbam") { + + 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), + 2, + 2 + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/bamutil/trimbam/tests/main.nf.test.snap b/modules/nf-core/bamutil/trimbam/tests/main.nf.test.snap new file mode 100644 index 00000000000..bebeabd6f8f --- /dev/null +++ b/modules/nf-core/bamutil/trimbam/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-bamutil-trimbam": { + "content": [ + "483cb3b74b338dcc04ea6ae53e86e179", + [ + "versions.yml:md5,db7889ac58ea4eeb68ceb652de159cc4" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T15:21:23.796158" + } +} \ No newline at end of file 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/clumpify/tests/main.nf.test b/modules/nf-core/bbmap/clumpify/tests/main.nf.test new file mode 100644 index 00000000000..f43b8767964 --- /dev/null +++ b/modules/nf-core/bbmap/clumpify/tests/main.nf.test @@ -0,0 +1,72 @@ + +nextflow_process { + + name "Test Process BBMAP_CLUMPIFY" + script "../main.nf" + process "BBMAP_CLUMPIFY" + + tag "modules" + tag "modules_nfcore" + tag "bbmap" + tag "bbmap/clumpify" + + test("test-bbmap-clumpify-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( + process.out.reads, + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-bbmap-clumpify-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( + process.out.reads, + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap b/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap new file mode 100644 index 00000000000..d2fa37f18c5 --- /dev/null +++ b/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap @@ -0,0 +1,49 @@ +{ + "test-bbmap-clumpify-paired-end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.clumped.fastq.gz:md5,27e51643262c1ef3905c4be184c3814c", + "test_2.clumped.fastq.gz:md5,c70ab7bbd44d6b6fadd6a1a79ef1648f" + ] + ] + ], + "test.clumpify.log", + [ + "versions.yml:md5,ec30171b7944e601f3fd733bb5408bf6" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T06:43:39.816170993" + }, + "test-bbmap-clumpify-single-end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.clumped.fastq.gz:md5,27e51643262c1ef3905c4be184c3814c" + ] + ], + "test.clumpify.log", + [ + "versions.yml:md5,ec30171b7944e601f3fd733bb5408bf6" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T06:43:28.923674245" + } +} \ 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/bbmap/sendsketch/meta.yml b/modules/nf-core/bbmap/sendsketch/meta.yml index 38a5fb3fe6a..76f3e9472ba 100644 --- a/modules/nf-core/bbmap/sendsketch/meta.yml +++ b/modules/nf-core/bbmap/sendsketch/meta.yml @@ -12,7 +12,7 @@ tools: description: "BBMap is a short read aligner, as well as various other bioinformatic 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/" - licence: "['UC-LBL license (see package)']" + licence: ["UC-LBL license (see package)"] input: - meta: type: map @@ -34,7 +34,7 @@ output: description: File containing software versions pattern: "versions.yml" - hits: - type: txt + type: file description: .txt file containing hits from a query seuqnce to various reference sequences output pattern: "*.{txt}" authors: diff --git a/modules/nf-core/bbmap/sendsketch/tests/main.nf.test b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test new file mode 100644 index 00000000000..744feadfcb1 --- /dev/null +++ b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test @@ -0,0 +1,70 @@ + +nextflow_process { + + name "Test Process BBMAP_SENDSKETCH" + script "../main.nf" + process "BBMAP_SENDSKETCH" + + tag "modules" + tag "modules_nfcore" + tag "bbmap" + tag "bbmap/sendsketch" + + test("test-bbmap-sendsketch-single") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.hits[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + + test("test-bbmap-sendsketch-paired") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.hits[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap new file mode 100644 index 00000000000..c516ae720ac --- /dev/null +++ b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap @@ -0,0 +1,40 @@ +{ + "test-bbmap-sendsketch-paired": { + "content": [ + [ + "0.52%\t0.14%\t82.66%\t.\t26.68%\t1.03%\t60\t10\t9534\t30656K\t46\tChlorocebus aethiops", + "0.46%\t0.12%\t82.30%\t.\t26.38%\t1.10%\t53\t7\t33548\t30986K\t46\tColobus guereza", + "9.02%\t0.03%\t91.56%\t.\t0.34%\t1.88%\t48\t8\t9606\t2387M\t26130\tHomo sapiens", + "0.30%\t0.08%\t80.90%\t.\t27.42%\t1.23%\t35\t8\t9523\t29749K\t44\tPlecturocebus moloch", + "6.70%\t0.02%\t90.53%\t.\t0.34%\t4.10%\t36\t0\t9595\t2355M\t5730\tGorilla gorilla gorilla" + ], + [ + "versions.yml:md5,694697087b868316aa450d1bc3775373" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:29:22.985067" + }, + "test-bbmap-sendsketch-single": { + "content": [ + [ + "0.66%\t0.53%\t83.30%\t.\t80.66%\t0.56%\t20\t17\t9593\t47555\t9\tGorilla gorilla", + "0.14%\t0.07%\t78.52%\t.\t48.11%\t1.09%\t4\t4\t27679\t78571\t4\tSaimiri boliviensis", + "7.69%\t0.01%\t90.45%\t.\t0.12%\t3.85%\t4\t1\t9534\t30656K\t46\tChlorocebus aethiops", + "0.17%\t0.04%\t79.27%\t.\t23.69%\t1.26%\t3\t1\t67082\t158942\t1\tBeAn 58058 virus", + "5.56%\t0.01%\t89.72%\t.\t0.12%\t5.56%\t3\t0\t9523\t29749K\t44\tPlecturocebus moloch" + ], + [ + "versions.yml:md5,694697087b868316aa450d1bc3775373" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T14:29:03.529673" + } +} \ 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/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/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/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/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/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/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/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/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/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/shiftfasta/tests/main.nf.test b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test new file mode 100644 index 00000000000..d11d144ea6e --- /dev/null +++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test @@ -0,0 +1,44 @@ + +nextflow_process { + + name "Test Process GATK4_SHIFTFASTA" + script "../main.nf" + process "GATK4_SHIFTFASTA" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/shiftfasta" + + test("test-gatk4-shiftfasta") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', 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/shiftfasta/tests/main.nf.test.snap b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap new file mode 100644 index 00000000000..bb7e5aa0191 --- /dev/null +++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap @@ -0,0 +1,133 @@ +{ + "test-gatk4-shiftfasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_shift.fasta:md5,d65f6e323b25f03a350651e040ad9823" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_shift.fasta.fai:md5,5324f610259af3846db7216b42626519" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_shift.back_chain:md5,513b4ccf3d1fe1578450795216a054ce" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test_shift.dict:md5,a46de767b35d329f438b682a3bc0d5a9" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.intervals:md5,2cf9d6be2fd5d65364526f9a4ec8cef0", + "test.shifted.intervals:md5,6d8d74cd94813e56ec9f09933884f45d" + ] + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test.shifted.intervals:md5,6d8d74cd94813e56ec9f09933884f45d" + ] + ], + "6": [ + "versions.yml:md5,afdffb5981aa10bdf40af3a50323fd54" + ], + "dict": [ + [ + { + "id": "test", + "single_end": false + }, + "test_shift.dict:md5,a46de767b35d329f438b682a3bc0d5a9" + ] + ], + "intervals": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.intervals:md5,2cf9d6be2fd5d65364526f9a4ec8cef0", + "test.shifted.intervals:md5,6d8d74cd94813e56ec9f09933884f45d" + ] + ] + ], + "shift_back_chain": [ + [ + { + "id": "test", + "single_end": false + }, + "test_shift.back_chain:md5,513b4ccf3d1fe1578450795216a054ce" + ] + ], + "shift_fa": [ + [ + { + "id": "test", + "single_end": false + }, + "test_shift.fasta:md5,d65f6e323b25f03a350651e040ad9823" + ] + ], + "shift_fai": [ + [ + { + "id": "test", + "single_end": false + }, + "test_shift.fasta.fai:md5,5324f610259af3846db7216b42626519" + ] + ], + "shift_intervals": [ + [ + { + "id": "test", + "single_end": false + }, + "test.shifted.intervals:md5,6d8d74cd94813e56ec9f09933884f45d" + ] + ], + "versions": [ + "versions.yml:md5,afdffb5981aa10bdf40af3a50323fd54" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T11:11:50.342225" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/shiftfasta/nextflow.config b/modules/nf-core/gatk4/shiftfasta/tests/nextflow.config similarity index 59% rename from tests/modules/nf-core/gatk4/shiftfasta/nextflow.config rename to modules/nf-core/gatk4/shiftfasta/tests/nextflow.config index bf109c3347b..de1be8e6b7d 100644 --- a/tests/modules/nf-core/gatk4/shiftfasta/nextflow.config +++ b/modules/nf-core/gatk4/shiftfasta/tests/nextflow.config @@ -1,7 +1,4 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'GATK4_SHIFTFASTA' { ext.args = "--intervals MT192765.1:576-16024 --shift-offset-list 8000 --interval-file-name test" } 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/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/last/dotplot/environment.yml b/modules/nf-core/last/dotplot/environment.yml index b013d4d8b0e..064a3a459da 100644 --- a/modules/nf-core/last/dotplot/environment.yml +++ b/modules/nf-core/last/dotplot/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::last=1542" + - "bioconda::last=1571" diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index 93f311d87cf..1ac3c9ff980 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -4,8 +4,8 @@ process LAST_DOTPLOT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' : - 'biocontainers/last:1542--h43eeafb_1' }" + 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' : + 'biocontainers/last:1571--h43eeafb_0' }" input: tuple val(meta), path(maf), path(annot_b) diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test.snap b/modules/nf-core/last/dotplot/tests/main.nf.test.snap index cff5b566404..41b3b7e92f7 100644 --- a/modules/nf-core/last/dotplot/tests/main.nf.test.snap +++ b/modules/nf-core/last/dotplot/tests/main.nf.test.snap @@ -2,37 +2,37 @@ "sarscov2 - contigs - genome - gif": { "content": [ [ - "versions.yml:md5,8a86fe4a0227c77ecfcc0aa21a3ece07" + "versions.yml:md5,2b5085f9eec6d9623d34b918b66ffe58" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-27T09:19:30.116358" + "timestamp": "2024-08-26T15:39:30.517622" }, "sarscov2 - contigs - genome - png - stub": { "content": [ [ - "versions.yml:md5,8a86fe4a0227c77ecfcc0aa21a3ece07" + "versions.yml:md5,2b5085f9eec6d9623d34b918b66ffe58" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-27T09:19:46.588825" + "timestamp": "2024-08-26T15:39:46.73375" }, "sarscov2 - contigs - genome - png": { "content": [ [ - "versions.yml:md5,8a86fe4a0227c77ecfcc0aa21a3ece07" + "versions.yml:md5,2b5085f9eec6d9623d34b918b66ffe58" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-27T09:19:08.959252" + "timestamp": "2024-08-26T15:39:14.058511" } } \ No newline at end of file diff --git a/modules/nf-core/last/lastal/environment.yml b/modules/nf-core/last/lastal/environment.yml index c3a87c68c1f..49f3e794c0c 100644 --- a/modules/nf-core/last/lastal/environment.yml +++ b/modules/nf-core/last/lastal/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::last=1542" + - "bioconda::last=1571" diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index 560ada11b32..470e87ccf1e 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -4,8 +4,8 @@ process LAST_LASTAL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' : - 'biocontainers/last:1542--h43eeafb_1' }" + 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' : + 'biocontainers/last:1571--h43eeafb_0' }" input: tuple val(meta), path(fastx), path (param_file) diff --git a/modules/nf-core/last/lastal/tests/main.nf.test.snap b/modules/nf-core/last/lastal/tests/main.nf.test.snap index 9245a96252e..d9a09c9aef6 100644 --- a/modules/nf-core/last/lastal/tests/main.nf.test.snap +++ b/modules/nf-core/last/lastal/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "id": "contigs", "single_end": false }, - "contigs.maf.gz:md5,902274b72657f62d270d284dc211aa7f" + "contigs.maf.gz:md5,dd02b4855c49bb3d46106177f5a08955" ] ], "1": [ @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2" + "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951" ], "maf": [ [ @@ -29,7 +29,7 @@ "id": "contigs", "single_end": false }, - "contigs.maf.gz:md5,902274b72657f62d270d284dc211aa7f" + "contigs.maf.gz:md5,dd02b4855c49bb3d46106177f5a08955" ] ], "multiqc": [ @@ -42,15 +42,15 @@ ] ], "versions": [ - "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2" + "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-02T17:57:48.589408" + "timestamp": "2024-08-26T15:23:20.411461" }, "sarscov2 - contigs - genome - stub": { "content": [ @@ -74,7 +74,7 @@ ] ], "2": [ - "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2" + "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951" ], "maf": [ [ @@ -95,15 +95,15 @@ ] ], "versions": [ - "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2" + "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-02T17:58:30.521811" + "timestamp": "2024-08-26T15:24:03.533878" }, "sarscov2 - contigs - genome - withparams": { "content": [ @@ -114,7 +114,7 @@ "id": "contigs", "single_end": false }, - "contigs.maf.gz:md5,8cb97b6daa34dbf9c723a2c4a984992d" + "contigs.maf.gz:md5,8e4058c39c8ea92da0fa063398b6346d" ] ], "1": [ @@ -127,7 +127,7 @@ ] ], "2": [ - "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2" + "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951" ], "maf": [ [ @@ -135,7 +135,7 @@ "id": "contigs", "single_end": false }, - "contigs.maf.gz:md5,8cb97b6daa34dbf9c723a2c4a984992d" + "contigs.maf.gz:md5,8e4058c39c8ea92da0fa063398b6346d" ] ], "multiqc": [ @@ -148,14 +148,14 @@ ] ], "versions": [ - "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2" + "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-02T17:58:09.677672" + "timestamp": "2024-08-26T15:23:42.107503" } } \ No newline at end of file diff --git a/modules/nf-core/last/lastdb/environment.yml b/modules/nf-core/last/lastdb/environment.yml index 9e98a10ae20..e8249083e74 100644 --- a/modules/nf-core/last/lastdb/environment.yml +++ b/modules/nf-core/last/lastdb/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::last=1542" + - "bioconda::last=1571" diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index 856b3643c77..916838450ae 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -4,8 +4,8 @@ process LAST_LASTDB { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' : - 'biocontainers/last:1542--h43eeafb_1' }" + 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' : + 'biocontainers/last:1571--h43eeafb_0' }" input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test.snap b/modules/nf-core/last/lastdb/tests/main.nf.test.snap index ee2a1130338..3ff3212f6f8 100644 --- a/modules/nf-core/last/lastdb/tests/main.nf.test.snap +++ b/modules/nf-core/last/lastdb/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "1": [ - "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557" + "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701" ], "index": [ [ @@ -38,15 +38,15 @@ ] ], "versions": [ - "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557" + "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-06T16:42:08.735561" + "timestamp": "2024-08-26T15:34:34.647102" }, "sarscov2 - fastq gzipped": { "content": [ @@ -59,7 +59,7 @@ [ "test.bck:md5,05b14d8ac418b3193d9cc921086cea05", "test.des:md5,26ab49015cc572172b9efa50fc5190bc", - "test.prj:md5,b50003077b7c7357fb8bacdf6f87653d", + "test.prj:md5,e668d4ee5fb0c2e9c82bd4a2fc3e7998", "test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b", "test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da", "test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0", @@ -68,7 +68,7 @@ ] ], "1": [ - "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557" + "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701" ], "index": [ [ @@ -78,7 +78,7 @@ [ "test.bck:md5,05b14d8ac418b3193d9cc921086cea05", "test.des:md5,26ab49015cc572172b9efa50fc5190bc", - "test.prj:md5,b50003077b7c7357fb8bacdf6f87653d", + "test.prj:md5,e668d4ee5fb0c2e9c82bd4a2fc3e7998", "test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b", "test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da", "test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0", @@ -87,15 +87,15 @@ ] ], "versions": [ - "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557" + "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-06T16:41:07.4512" + "timestamp": "2024-08-26T15:34:18.336299" }, "sarscov2 - fasta": { "content": [ @@ -108,7 +108,7 @@ [ "test.bck:md5,157526d333b88523cb15ac4efe00738f", "test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc", - "test.prj:md5,b937b1565cb4c983c8fcd3780d3e151e", + "test.prj:md5,f7e7445a3ff008efe127ca841f59fe9c", "test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015", "test.ssp:md5,53524efdea3d8989201419a29e81ec1f", "test.suf:md5,ef7482260705bb8146acbbbdce6c0068", @@ -117,7 +117,7 @@ ] ], "1": [ - "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557" + "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701" ], "index": [ [ @@ -127,7 +127,7 @@ [ "test.bck:md5,157526d333b88523cb15ac4efe00738f", "test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc", - "test.prj:md5,b937b1565cb4c983c8fcd3780d3e151e", + "test.prj:md5,f7e7445a3ff008efe127ca841f59fe9c", "test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015", "test.ssp:md5,53524efdea3d8989201419a29e81ec1f", "test.suf:md5,ef7482260705bb8146acbbbdce6c0068", @@ -136,14 +136,14 @@ ] ], "versions": [ - "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557" + "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-06T16:40:05.874954" + "timestamp": "2024-08-26T15:34:01.800286" } } \ No newline at end of file diff --git a/modules/nf-core/last/mafconvert/environment.yml b/modules/nf-core/last/mafconvert/environment.yml index 009cb82f4ac..9aea0cbe6ee 100644 --- a/modules/nf-core/last/mafconvert/environment.yml +++ b/modules/nf-core/last/mafconvert/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::last=1542" + - "bioconda::last=1571" diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index 3bed0600bf8..bbe6c75d9a6 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -4,8 +4,8 @@ process LAST_MAFCONVERT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' : - 'biocontainers/last:1542--h43eeafb_1' }" + 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' : + 'biocontainers/last:1571--h43eeafb_0' }" input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafconvert/tests/main.nf.test.snap b/modules/nf-core/last/mafconvert/tests/main.nf.test.snap index 3693b980836..f1c41c08189 100644 --- a/modules/nf-core/last/mafconvert/tests/main.nf.test.snap +++ b/modules/nf-core/last/mafconvert/tests/main.nf.test.snap @@ -35,7 +35,7 @@ ], "9": [ - "versions.yml:md5,d759c732b33af95ef94f98c01fcc041b" + "versions.yml:md5,4e515249c766dcf398f517bb837adce5" ], "axt_gz": [ @@ -70,15 +70,15 @@ ], "versions": [ - "versions.yml:md5,d759c732b33af95ef94f98c01fcc041b" + "versions.yml:md5,4e515249c766dcf398f517bb837adce5" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-06T18:12:33.604233" + "timestamp": "2024-08-26T15:26:55.89707" }, "sarscov2 - bam": { "content": [ @@ -116,7 +116,7 @@ ], "9": [ - "versions.yml:md5,d759c732b33af95ef94f98c01fcc041b" + "versions.yml:md5,4e515249c766dcf398f517bb837adce5" ], "axt_gz": [ @@ -151,14 +151,14 @@ ], "versions": [ - "versions.yml:md5,d759c732b33af95ef94f98c01fcc041b" + "versions.yml:md5,4e515249c766dcf398f517bb837adce5" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-06T18:11:32.396233" + "timestamp": "2024-08-26T15:26:39.429173" } } \ No newline at end of file diff --git a/modules/nf-core/last/mafswap/environment.yml b/modules/nf-core/last/mafswap/environment.yml index cc112af83d4..15e3c6b8ba5 100644 --- a/modules/nf-core/last/mafswap/environment.yml +++ b/modules/nf-core/last/mafswap/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::last=1542" + - "bioconda::last=1571" diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index 875a6af3498..4dadf391ff4 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -4,8 +4,8 @@ process LAST_MAFSWAP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' : - 'biocontainers/last:1542--h43eeafb_1' }" + 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' : + 'biocontainers/last:1571--h43eeafb_0' }" input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafswap/tests/main.nf.test.snap b/modules/nf-core/last/mafswap/tests/main.nf.test.snap index cc085dffe1b..5c41a422a0b 100644 --- a/modules/nf-core/last/mafswap/tests/main.nf.test.snap +++ b/modules/nf-core/last/mafswap/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,9819f8873c15cc665cbee998cefb72dd" + "versions.yml:md5,1a6fc970e6952d90c3b560162af8fb1f" ], "maf": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,9819f8873c15cc665cbee998cefb72dd" + "versions.yml:md5,1a6fc970e6952d90c3b560162af8fb1f" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-04T17:59:43.47396" + "timestamp": "2024-08-26T15:31:41.694631" }, "sarscov2 - contigs - genome - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,9819f8873c15cc665cbee998cefb72dd" + "versions.yml:md5,1a6fc970e6952d90c3b560162af8fb1f" ], "maf": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,9819f8873c15cc665cbee998cefb72dd" + "versions.yml:md5,1a6fc970e6952d90c3b560162af8fb1f" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-06T19:41:29.891962" + "timestamp": "2024-08-26T15:31:58.257208" } } \ No newline at end of file diff --git a/modules/nf-core/last/postmask/environment.yml b/modules/nf-core/last/postmask/environment.yml index 75ee281150d..899e8fee491 100644 --- a/modules/nf-core/last/postmask/environment.yml +++ b/modules/nf-core/last/postmask/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::last=1542" + - "bioconda::last=1571" diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index ed2b5f0c060..e9ff4878fde 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -4,8 +4,8 @@ process LAST_POSTMASK { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' : - 'biocontainers/last:1542--h43eeafb_1' }" + 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' : + 'biocontainers/last:1571--h43eeafb_0' }" input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/postmask/tests/main.nf.test.snap b/modules/nf-core/last/postmask/tests/main.nf.test.snap index 3d924744615..3af5efbc4b8 100644 --- a/modules/nf-core/last/postmask/tests/main.nf.test.snap +++ b/modules/nf-core/last/postmask/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,5bfe6a9059961e1533daf7a021899249" + "versions.yml:md5,d1f6eee514bd694a0aeead8ee815a19e" ], "maf": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,5bfe6a9059961e1533daf7a021899249" + "versions.yml:md5,d1f6eee514bd694a0aeead8ee815a19e" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-03T15:21:37.870786" + "timestamp": "2024-08-26T15:36:54.898194" }, "sarscov2 - contigs - genome - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,5bfe6a9059961e1533daf7a021899249" + "versions.yml:md5,d1f6eee514bd694a0aeead8ee815a19e" ], "maf": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,5bfe6a9059961e1533daf7a021899249" + "versions.yml:md5,d1f6eee514bd694a0aeead8ee815a19e" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-06-06T19:55:47.691726" + "timestamp": "2024-08-26T15:37:11.363434" } } \ No newline at end of file diff --git a/modules/nf-core/last/split/environment.yml b/modules/nf-core/last/split/environment.yml index 7d76b55fca1..c4608dd218c 100644 --- a/modules/nf-core/last/split/environment.yml +++ b/modules/nf-core/last/split/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::last=1542" + - "bioconda::last=1571" diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index 410d16f1d27..9fcf3588d57 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -4,8 +4,8 @@ process LAST_SPLIT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' : - 'biocontainers/last:1542--h43eeafb_1' }" + 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' : + 'biocontainers/last:1571--h43eeafb_0' }" input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/tests/main.nf.test.snap b/modules/nf-core/last/split/tests/main.nf.test.snap index 953a6542a80..603f9263f5a 100644 --- a/modules/nf-core/last/split/tests/main.nf.test.snap +++ b/modules/nf-core/last/split/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1" + "versions.yml:md5,8b705a62c76f7753a51d3d387cf458f1" ], "maf": [ [ @@ -38,15 +38,15 @@ ] ], "versions": [ - "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1" + "versions.yml:md5,8b705a62c76f7753a51d3d387cf458f1" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-02T11:45:00.535348" + "timestamp": "2024-08-26T15:20:43.307807" }, "sarscov2 - contigs_genome - stub": { "content": [ @@ -68,7 +68,7 @@ ] ], "2": [ - "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1" + "versions.yml:md5,8b705a62c76f7753a51d3d387cf458f1" ], "maf": [ [ @@ -87,14 +87,14 @@ ] ], "versions": [ - "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1" + "versions.yml:md5,8b705a62c76f7753a51d3d387cf458f1" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-02T11:45:21.243325" + "timestamp": "2024-08-26T15:20:59.963034" } } \ No newline at end of file diff --git a/modules/nf-core/last/train/environment.yml b/modules/nf-core/last/train/environment.yml index 5edaf64fdfc..1a59871b7a5 100644 --- a/modules/nf-core/last/train/environment.yml +++ b/modules/nf-core/last/train/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::last=1542" + - "bioconda::last=1571" diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index 9f592b56e38..0829060f4ba 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -4,8 +4,8 @@ process LAST_TRAIN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' : - 'biocontainers/last:1542--h43eeafb_1' }" + 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' : + 'biocontainers/last:1571--h43eeafb_0' }" input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/train/tests/main.nf.test.snap b/modules/nf-core/last/train/tests/main.nf.test.snap index a3a0cc8f000..0c9185d5216 100644 --- a/modules/nf-core/last/train/tests/main.nf.test.snap +++ b/modules/nf-core/last/train/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,c5578547acf9e77e1e8f6bf796e32ac2" + "versions.yml:md5,0a9cfea9e8b841939e040ff6d45de96f" ], "multiqc": [ [ @@ -42,15 +42,15 @@ ] ], "versions": [ - "versions.yml:md5,c5578547acf9e77e1e8f6bf796e32ac2" + "versions.yml:md5,0a9cfea9e8b841939e040ff6d45de96f" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T14:50:11.528587" + "timestamp": "2024-08-26T15:29:24.633162" }, "sarscov2 - genome - contigs": { "content": [ @@ -61,7 +61,7 @@ "id": "contigs", "single_end": false }, - "contigs.genome.train:md5,3d7e1c630705d83c6a11b6f28d5aefcb" + "contigs.genome.train:md5,c269b6fee0f0b3011c4cb2764645955c" ] ], "1": [ @@ -74,7 +74,7 @@ ] ], "2": [ - "versions.yml:md5,38234cf053c708e57cc080990f777411" + "versions.yml:md5,1d8eb88ebe5170b8a0e561f5a3491f0e" ], "multiqc": [ [ @@ -91,18 +91,18 @@ "id": "contigs", "single_end": false }, - "contigs.genome.train:md5,3d7e1c630705d83c6a11b6f28d5aefcb" + "contigs.genome.train:md5,c269b6fee0f0b3011c4cb2764645955c" ] ], "versions": [ - "versions.yml:md5,38234cf053c708e57cc080990f777411" + "versions.yml:md5,1d8eb88ebe5170b8a0e561f5a3491f0e" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T18:04:34.914789" + "timestamp": "2024-08-26T15:29:03.278235" } } \ No newline at end of file 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/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 f4ce031ef77..11dd9514e35 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -25,39 +25,15 @@ ataqv/ataqv: ataqv/mkarv: - modules/nf-core/ataqv/mkarv/** - tests/modules/nf-core/ataqv/mkarv/** -atlas/call: - - modules/nf-core/atlas/call/** - - tests/modules/nf-core/atlas/call/** -atlas/pmd: - - modules/nf-core/atlas/pmd/** - - tests/modules/nf-core/atlas/pmd/** -atlas/recal: - - modules/nf-core/atlas/recal/** - - tests/modules/nf-core/atlas/recal/** -atlas/splitmerge: - - modules/nf-core/atlas/splitmerge/** - - tests/modules/nf-core/atlas/splitmerge/** authentict/deam2cont: - modules/nf-core/authentict/deam2cont/** - tests/modules/nf-core/authentict/deam2cont/** -bam2fastx/bam2fastq: - - modules/nf-core/bam2fastx/bam2fastq/** - - tests/modules/nf-core/bam2fastx/bam2fastq/** bamtools/convert: - modules/nf-core/bamtools/convert/** - tests/modules/nf-core/bamtools/convert/** bamtools/split: - modules/nf-core/bamtools/split/** - tests/modules/nf-core/bamtools/split/** -bamtools/stats: - - modules/nf-core/bamtools/stats/** - - tests/modules/nf-core/bamtools/stats/** -bamutil/trimbam: - - modules/nf-core/bamutil/trimbam/** - - tests/modules/nf-core/bamutil/trimbam/** -bandage/image: - - modules/nf-core/bandage/image/** - - tests/modules/nf-core/bandage/image/** basicpy: - modules/nf-core/basicpy/** - tests/modules/nf-core/basicpy/** @@ -67,63 +43,30 @@ bbmap/align: bbmap/bbnorm: - modules/nf-core/bbmap/bbnorm/** - tests/modules/nf-core/bbmap/bbnorm/** -bbmap/clumpify: - - modules/nf-core/bbmap/clumpify/** - - tests/modules/nf-core/bbmap/clumpify/** 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/** -bbmap/sendsketch: - - modules/nf-core/bbmap/sendsketch/** - - tests/modules/nf-core/bbmap/sendsketch/** 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/** @@ -434,27 +377,15 @@ 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/** @@ -467,18 +398,12 @@ 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/** @@ -488,39 +413,21 @@ 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/** @@ -620,9 +527,6 @@ 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/** @@ -650,9 +554,6 @@ 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/** @@ -1064,9 +965,6 @@ picard/filtersamreads: picard/fixmateinformation: - modules/nf-core/picard/fixmateinformation/** - tests/modules/nf-core/picard/fixmateinformation/** -picard/renamesampleinvcf: - - modules/nf-core/picard/renamesampleinvcf/** - - tests/modules/nf-core/picard/renamesampleinvcf/** picard/scatterintervalsbyns: - modules/nf-core/picard/scatterintervalsbyns/** - tests/modules/nf-core/picard/scatterintervalsbyns/** diff --git a/tests/modules/nf-core/atlas/call/main.nf b/tests/modules/nf-core/atlas/call/main.nf deleted file mode 100644 index 5e2320b2c11..00000000000 --- a/tests/modules/nf-core/atlas/call/main.nf +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ATLAS_CALL } from '../../../../../modules/nf-core/atlas/call/main.nf' - -workflow test_atlas_call { - - 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 = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - known_alleles = [] - method = 'randomBase' - - ATLAS_CALL ( input, fasta, fai, known_alleles, method ) -} diff --git a/tests/modules/nf-core/atlas/call/nextflow.config b/tests/modules/nf-core/atlas/call/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/atlas/call/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/atlas/call/test.yml b/tests/modules/nf-core/atlas/call/test.yml deleted file mode 100644 index 78549fa3feb..00000000000 --- a/tests/modules/nf-core/atlas/call/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: atlas call test_atlas_call - command: nextflow run ./tests/modules/nf-core/atlas/call -entry test_atlas_call -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/atlas/call/nextflow.config - tags: - - atlas - - atlas/call - files: - - path: output/atlas/test.paired_end.sorted_randomBase.vcf.gz - contains: - - "##source=atlas" diff --git a/tests/modules/nf-core/atlas/pmd/main.nf b/tests/modules/nf-core/atlas/pmd/main.nf deleted file mode 100644 index bcba7dc3f4f..00000000000 --- a/tests/modules/nf-core/atlas/pmd/main.nf +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ATLAS_PMD } from '../../../../../modules/nf-core/atlas/pmd/main.nf' - -workflow test_atlas_pmd { - - 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) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - - ATLAS_PMD ( input, fasta, fai ) -} diff --git a/tests/modules/nf-core/atlas/pmd/nextflow.config b/tests/modules/nf-core/atlas/pmd/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/atlas/pmd/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/atlas/pmd/test.yml b/tests/modules/nf-core/atlas/pmd/test.yml deleted file mode 100644 index bb2c3f973ac..00000000000 --- a/tests/modules/nf-core/atlas/pmd/test.yml +++ /dev/null @@ -1,14 +0,0 @@ -- name: atlas pmd test_atlas_pmd - command: nextflow run ./tests/modules/nf-core/atlas/pmd -entry test_atlas_pmd -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/atlas/pmd/nextflow.config - tags: - - atlas/pmd - - atlas - files: - - path: output/atlas/test.paired_end.sorted_PMD_Table.txt - md5sum: b28a9f4784f30a711046708eb7d94642 - - path: output/atlas/test.paired_end.sorted_PMD_Table_counts.txt - md5sum: 1aabfb83cfff6e0413f52d016c943e3e - - path: output/atlas/test.paired_end.sorted_PMD_input_Empiric.txt - md5sum: 8ff876f50ce05dc9aac0646a31682df0 - - path: output/atlas/test.paired_end.sorted_PMD_input_Exponential.txt - md5sum: 2421450ef643316f4eacf5cb811e4df7 diff --git a/tests/modules/nf-core/atlas/recal/main.nf b/tests/modules/nf-core/atlas/recal/main.nf deleted file mode 100644 index fadda2019e6..00000000000 --- a/tests/modules/nf-core/atlas/recal/main.nf +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ATLAS_RECAL } from '../../../../../modules/nf-core/atlas/recal/main.nf' - -workflow test_atlas_recal { - - 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), - [], - [] - ] - alleles = [] - invariant_sites = [] - - ATLAS_RECAL ( input, alleles, invariant_sites ) -} - - diff --git a/tests/modules/nf-core/atlas/recal/nextflow.config b/tests/modules/nf-core/atlas/recal/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/atlas/recal/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/atlas/recal/test.yml b/tests/modules/nf-core/atlas/recal/test.yml deleted file mode 100644 index a18b22c01dc..00000000000 --- a/tests/modules/nf-core/atlas/recal/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: atlas recal test_atlas_recal - command: nextflow run ./tests/modules/nf-core/atlas/recal -entry test_atlas_recal -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/atlas/recal/nextflow.config - tags: - - atlas/recal - - atlas - files: - - path: output/atlas/test_recalibrationEM.txt - contains: ["readGroup"] diff --git a/tests/modules/nf-core/atlas/splitmerge/main.nf b/tests/modules/nf-core/atlas/splitmerge/main.nf deleted file mode 100644 index bde3c197329..00000000000 --- a/tests/modules/nf-core/atlas/splitmerge/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ATLAS_SPLITMERGE } from '../../../../../modules/nf-core/atlas/splitmerge/main.nf' - -//MAIN -workflow test_atlas_splitmerge { - meta = [ id:'test', single_end:false ] - bam = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - bai = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - settings = file(params.test_data['homo_sapiens']['illumina']['read_group_settings_txt'], checkIfExists: true) - - ATLAS_SPLITMERGE ( [meta, bam, bai, settings, []] ) -} diff --git a/tests/modules/nf-core/atlas/splitmerge/nextflow.config b/tests/modules/nf-core/atlas/splitmerge/nextflow.config deleted file mode 100644 index ff5bc70147a..00000000000 --- a/tests/modules/nf-core/atlas/splitmerge/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: ATLAS_SPLITMERGE { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - } -} \ No newline at end of file diff --git a/tests/modules/nf-core/atlas/splitmerge/test.yml b/tests/modules/nf-core/atlas/splitmerge/test.yml deleted file mode 100644 index c41c8e06a69..00000000000 --- a/tests/modules/nf-core/atlas/splitmerge/test.yml +++ /dev/null @@ -1,11 +0,0 @@ -- name: atlas splitmerge test_atlas_splitmerge - command: nextflow run ./tests/modules/nf-core/atlas/splitmerge -entry test_atlas_splitmerge -c ./tests/config/nextflow.config - tags: - - atlas - - atlas/splitmerge - files: - - path: output/atlas/test.paired_end.sorted_ignoredReads.txt.gz - md5sum: 9b64c47313d2de89c26790f713707ee6 - - path: output/atlas/test.paired_end.sorted_mergedReads.bam - - path: output/atlas/versions.yml - md5sum: 11735bec9c2f4b395b987fd00d4e4294 diff --git a/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf b/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf deleted file mode 100644 index d8073765b6d..00000000000 --- a/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BAM2FASTX_BAM2FASTQ } from '../../../../../modules/nf-core/bam2fastx/bam2fastq/main.nf' - -workflow test_bam2fastx_bam2fastq { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['alz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['pacbio']['alzpbi'], checkIfExists: true) - ] - - BAM2FASTX_BAM2FASTQ ( input ) -} diff --git a/tests/modules/nf-core/bam2fastx/bam2fastq/nextflow.config b/tests/modules/nf-core/bam2fastx/bam2fastq/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/bam2fastx/bam2fastq/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/bam2fastx/bam2fastq/test.yml b/tests/modules/nf-core/bam2fastx/bam2fastq/test.yml deleted file mode 100644 index 18b9f144a72..00000000000 --- a/tests/modules/nf-core/bam2fastx/bam2fastq/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: bam2fastx bam2fastq test_bam2fastx_bam2fastq - command: nextflow run ./tests/modules/nf-core/bam2fastx/bam2fastq -entry test_bam2fastx_bam2fastq -c ./tests/config/nextflow.config - tags: - - bam2fastx/bam2fastq - - bam2fastx - files: - - path: output/bam2fastx/test.fastq.gz - md5sum: f0329f9ea12324c6631ac9f3712f2ca5 - - path: output/bam2fastx/versions.yml diff --git a/tests/modules/nf-core/bamtools/stats/main.nf b/tests/modules/nf-core/bamtools/stats/main.nf deleted file mode 100644 index 6adbb060bea..00000000000 --- a/tests/modules/nf-core/bamtools/stats/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BAMTOOLS_STATS } from '../../../../../modules/nf-core/bamtools/stats/main.nf' - -workflow test_bamtools_stats { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - BAMTOOLS_STATS ( input ) -} diff --git a/tests/modules/nf-core/bamtools/stats/nextflow.config b/tests/modules/nf-core/bamtools/stats/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/bamtools/stats/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/bamtools/stats/test.yml b/tests/modules/nf-core/bamtools/stats/test.yml deleted file mode 100644 index b8bd38e44bd..00000000000 --- a/tests/modules/nf-core/bamtools/stats/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: bamtools stats test_bamtools_stats - command: nextflow run ./tests/modules/nf-core/bamtools/stats -entry test_bamtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamtools/stats/nextflow.config - tags: - - bamtools - - bamtools/stats - files: - - path: output/bamtools/test.bam.stats - md5sum: b7c3f01682673a652d664a2889b15b66 - - path: output/bamtools/versions.yml diff --git a/tests/modules/nf-core/bamutil/trimbam/main.nf b/tests/modules/nf-core/bamutil/trimbam/main.nf deleted file mode 100644 index b2359338d88..00000000000 --- a/tests/modules/nf-core/bamutil/trimbam/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BAMUTIL_TRIMBAM } from '../../../../../modules/nf-core/bamutil/trimbam/main.nf' - -workflow test_bamutil_trimbam { - - input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), - 2, - 2 ] - - BAMUTIL_TRIMBAM ( input ) -} diff --git a/tests/modules/nf-core/bamutil/trimbam/nextflow.config b/tests/modules/nf-core/bamutil/trimbam/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/bamutil/trimbam/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/bamutil/trimbam/test.yml b/tests/modules/nf-core/bamutil/trimbam/test.yml deleted file mode 100644 index ec9371afd74..00000000000 --- a/tests/modules/nf-core/bamutil/trimbam/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: bamutil trimbam test_bamutil_trimbam - command: nextflow run ./tests/modules/nf-core/bamutil/trimbam -entry test_bamutil_trimbam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamutil/trimbam/nextflow.config - tags: - - bamutil/trimbam - - bamutil - files: - - path: output/bamutil/test.bam - md5sum: 9ddd0ecca82f7f3433383f3d1308970e 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/clumpify/main.nf b/tests/modules/nf-core/bbmap/clumpify/main.nf deleted file mode 100644 index 65b49acce8e..00000000000 --- a/tests/modules/nf-core/bbmap/clumpify/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BBMAP_CLUMPIFY } from '../../../../../modules/nf-core/bbmap/clumpify/main.nf' - -workflow test_bbmap_clumpify_single_end { - - input = [ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] - - BBMAP_CLUMPIFY ( input ) -} - -workflow test_bbmap_clumpify_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) ] - ] - - BBMAP_CLUMPIFY ( input ) -} diff --git a/tests/modules/nf-core/bbmap/clumpify/nextflow.config b/tests/modules/nf-core/bbmap/clumpify/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/bbmap/clumpify/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/clumpify/test.yml b/tests/modules/nf-core/bbmap/clumpify/test.yml deleted file mode 100644 index 65975b4f70d..00000000000 --- a/tests/modules/nf-core/bbmap/clumpify/test.yml +++ /dev/null @@ -1,18 +0,0 @@ -- name: bbmap clumpify test_bbmap_clumpify_single_end - command: nextflow run ./tests/modules/nf-core/bbmap/clumpify -entry test_bbmap_clumpify_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/clumpify/nextflow.config - tags: - - bbmap/clumpify - - bbmap - files: - - path: output/bbmap/test.clumped.fastq.gz - - path: output/bbmap/test.clumpify.log - -- name: bbmap clumpify test_bbmap_clumpify_paired_end - command: nextflow run ./tests/modules/nf-core/bbmap/clumpify -entry test_bbmap_clumpify_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/clumpify/nextflow.config - tags: - - bbmap/clumpify - - bbmap - files: - - path: output/bbmap/test.clumpify.log - - path: output/bbmap/test_1.clumped.fastq.gz - - path: output/bbmap/test_2.clumped.fastq.gz 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/bbmap/sendsketch/main.nf b/tests/modules/nf-core/bbmap/sendsketch/main.nf deleted file mode 100644 index dafc331573b..00000000000 --- a/tests/modules/nf-core/bbmap/sendsketch/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BBMAP_SENDSKETCH } from '../../../../../modules/nf-core/bbmap/sendsketch/main.nf' - -workflow test_bbmap_sendsketch_single { - - input = [ [ id:'test', single_end:true], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - ] - - BBMAP_SENDSKETCH ( input ) -} - -workflow test_bbmap_sendsketch_paired { - - input = [ [ id:'test', single_end:false], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test2_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_2_fastq_gz'], checkIfExists: true) - ] - ] - - BBMAP_SENDSKETCH ( input ) -} - diff --git a/tests/modules/nf-core/bbmap/sendsketch/nextflow.config b/tests/modules/nf-core/bbmap/sendsketch/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/bbmap/sendsketch/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/sendsketch/test.yml b/tests/modules/nf-core/bbmap/sendsketch/test.yml deleted file mode 100644 index ffbb1d77327..00000000000 --- a/tests/modules/nf-core/bbmap/sendsketch/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: bbmap sendsketch test_bbmap_sendsketch_single - command: nextflow run ./tests/modules/nf-core/bbmap/sendsketch -entry test_bbmap_sendsketch_single -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/sendsketch/nextflow.config - tags: - - bbmap/sendsketch - - bbmap - files: - - path: output/bbmap/test.txt - md5sum: ba6a78659eb15d0d130d5daee8c87ead - - path: output/bbmap/versions.yml - -- name: bbmap sendsketch test_bbmap_sendsketch_paired - command: nextflow run ./tests/modules/nf-core/bbmap/sendsketch -entry test_bbmap_sendsketch_paired -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/sendsketch/nextflow.config - tags: - - bbmap/sendsketch - - bbmap - files: - - path: output/bbmap/test.txt - md5sum: 651f7321cd0340844d23a1457a9651f9 - - path: output/bbmap/versions.yml 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/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/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/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/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/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/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/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/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/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/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/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/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/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