diff --git a/CHANGELOG.md b/CHANGELOG.md index 15da8cb59..33b18a92c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -96,7 +96,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Changed local `ARRIBA_VISUALIZATION`, `CTATSPLICING_STARTOCANCERINTRONS`, `CTATSPLICING_PREPGENOMELIB`, `FUSIONINSPECTOR`, `STARFUSION_DETECT` for its nf-core module versions [#740](https://github.com/nf-core/rnafusion/pull/740) - Replaced local subworkflow `TRIM_WORKFLOW` for its nf-core subworkflow equivalent `FASTQ_FASTQC_UMITOOLS_FASTP` [#752](https://github.com/nf-core/rnafusion/pull/752) - Changed local `FASTQ_ALIGN_STAR` for subworkflow from nf-core [#756](https://github.com/nf-core/rnafusion/pull/756) -- Replaced local subworkflow `STRINGTIE_WORKFLOW` for its nf-core version `BAM_STRINGTIE_MERGE` and the local module module `GTF_TO_REFFLAT` for nf-core's `UCSC_GTFTOGENEPRED` [#758](https://github.com/nf-core/rnafusion/pull/758) +- Replaced local subworkflow `STRINGTIE_WORKFLOW` for its nf-core version `BAM_STRINGTIE_MERGE` and the local module module `GTF_TO_REFFLAT` for nf-core's `UCSC_GTFTOGENEPRED` [#758](https://github.com/nf-core/rnafusion/pull/758 +- Update modules and close todos as preparation for release [#759](https://github.com/nf-core/rnafusion/pull/759) ### Fixed diff --git a/README.md b/README.md index 6da8f3b1a..6f1a9fd19 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.2565517-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.2565517) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) diff --git a/modules.json b/modules.json index c3555ee44..9505147f7 100644 --- a/modules.json +++ b/modules.json @@ -12,12 +12,12 @@ }, "agat/convertspgff2tsv": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "arriba/arriba": { "branch": "master", - "git_sha": "077818897bfe993e1ed91a0339bcbe53fe13edc7", + "git_sha": "025a6f75e1f72e4ab60abb4bd65b3f289d4ad910", "installed_by": ["modules"] }, "arriba/visualisation": { @@ -32,12 +32,12 @@ }, "cat/cat": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "ctatsplicing/prepgenomelib": { @@ -54,7 +54,7 @@ }, "fastp": { "branch": "master", - "git_sha": "d082103d7976a2804f21225446cc110cbd822f4c", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "fastqc": { @@ -84,62 +84,62 @@ }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b", "installed_by": ["modules"] }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "1ec937ab3edc307bc0d79a2200d784e9f0868359", + "git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b", "installed_by": ["modules"] }, "gffread": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "a4488d3d09244f29fb4606ba4eef85d59dcc6ad8", "installed_by": ["modules"] }, "picard/collectinsertsizemetrics": { "branch": "master", - "git_sha": "980a4964be91da75fb3ccf576118a18e247f6d15", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "picard/collectrnaseqmetrics": { "branch": "master", - "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "picard/collectwgsmetrics": { "branch": "master", - "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "salmon/index": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "salmon/quant": { "branch": "master", - "git_sha": "db5a84497b80c4932b4498ec231f19403d19bcff", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "samtools/flagstat": { @@ -154,7 +154,7 @@ }, "samtools/index": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/sort": { @@ -169,17 +169,17 @@ }, "star/align": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["fastq_align_star", "modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "starfusion/build": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "310a7a59c7f2362d25070e5928f3139f92377eaf", "installed_by": ["modules"] }, "starfusion/detect": { @@ -189,17 +189,17 @@ }, "stringtie/merge": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["bam_stringtie_merge", "modules"] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["bam_stringtie_merge", "modules"] }, "ucsc/gtftogenepred": { "branch": "master", - "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "umitools/extract": { @@ -238,17 +238,17 @@ }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", + "git_sha": "dcd088f483cede0c3df4034d405126f05a764cc7", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/agat/convertspgff2tsv/main.nf b/modules/nf-core/agat/convertspgff2tsv/main.nf index 772c7bd0b..d2b9b8608 100644 --- a/modules/nf-core/agat/convertspgff2tsv/main.nf +++ b/modules/nf-core/agat/convertspgff2tsv/main.nf @@ -18,13 +18,13 @@ process AGAT_CONVERTSPGFF2TSV { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ agat_convert_sp_gff2tsv.pl \\ - --gff $gff \\ + --gff ${gff} \\ --output ${prefix}.tsv \\ - $args + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/agat/convertspgff2tsv/meta.yml b/modules/nf-core/agat/convertspgff2tsv/meta.yml index 31f098683..4c80ee890 100644 --- a/modules/nf-core/agat/convertspgff2tsv/meta.yml +++ b/modules/nf-core/agat/convertspgff2tsv/meta.yml @@ -27,21 +27,27 @@ input: type: file description: Annotation file in GFF3/GTF format pattern: "*.{gff, gtf}" + ontologies: + - edam: "http://edamontology.org/format_1975" # GFF3 + - edam: "http://edamontology.org/format_2306" # GTF output: - - tsv: - - meta: - type: file - description: Annotation file in TSV format - pattern: "*.{gtf}" + tsv: + - - meta: + type: map + description: Groovy Map containing sample information - "*.tsv": type: file description: Annotation file in TSV format pattern: "*.{gtf}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_2306 # GTF + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: "http://edamontology.org/format_3750" # YAML authors: - "@rannick" maintainers: diff --git a/modules/nf-core/arriba/arriba/meta.yml b/modules/nf-core/arriba/arriba/meta.yml index 91ba21039..967f83756 100644 --- a/modules/nf-core/arriba/arriba/meta.yml +++ b/modules/nf-core/arriba/arriba/meta.yml @@ -25,6 +25,7 @@ input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + ontologies: [] - - meta2: type: map description: | @@ -34,6 +35,7 @@ input: type: file description: Assembly FASTA file pattern: "*.{fasta}" + ontologies: [] - - meta3: type: map description: | @@ -43,25 +45,33 @@ input: type: file description: Annotation GTF file pattern: "*.{gtf}" - - - blacklist: - type: file - description: Blacklist file - pattern: "*.{tsv}" - - - known_fusions: - type: file - description: Known fusions file - pattern: "*.{tsv}" - - - cytobands: - type: file - description: Cytobands file - pattern: "*.{tsv}" - - - protein_domains: - type: file - description: Protein domains file - pattern: "*.{gff3}" + ontologies: [] + - blacklist: + type: file + description: Blacklist file + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - known_fusions: + type: file + description: Known fusions file + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - cytobands: + type: file + description: Cytobands file + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - protein_domains: + type: file + description: Protein domains file + pattern: "*.{gff3}" + ontologies: [] output: - - fusions: - - meta: + fusions: + - - meta: type: map description: | Groovy Map containing sample information @@ -70,8 +80,9 @@ output: type: file description: File contains fusions which pass all of Arriba's filters. pattern: "*.{fusions.tsv}" - - fusions_fail: - - meta: + ontologies: [] + fusions_fail: + - - meta: type: map description: | Groovy Map containing sample information @@ -81,11 +92,14 @@ output: description: File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue. pattern: "*.{fusions.discarded.tsv}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@praveenraj2018" - "@rannick" diff --git a/modules/nf-core/arriba/arriba/tests/main.nf.test b/modules/nf-core/arriba/arriba/tests/main.nf.test index e76c06871..b5f404134 100644 --- a/modules/nf-core/arriba/arriba/tests/main.nf.test +++ b/modules/nf-core/arriba/arriba/tests/main.nf.test @@ -13,6 +13,81 @@ nextflow_process { tag "star/genomegenerate" tag "star/align" + test("arriba - homo_sapiens - paired_end") { + config "./nextflow.config" + + setup{ + run("STAR_GENOMEGENERATE") { + script '../../../star/genomegenerate/main.nf' + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + + run("STAR_ALIGN") { + script '../../../star/align/main.nf' + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + } + + when { + process { + """ + input[0] = STAR_ALIGN.out.bam + input[1] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = [] + + input[4] = [] + + input[5] = [] + + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("arriba - homo_sapiens - paired_end - stub") { options "-stub" diff --git a/modules/nf-core/arriba/arriba/tests/main.nf.test.snap b/modules/nf-core/arriba/arriba/tests/main.nf.test.snap index 7cf286a2f..ad3e7aa9c 100644 --- a/modules/nf-core/arriba/arriba/tests/main.nf.test.snap +++ b/modules/nf-core/arriba/arriba/tests/main.nf.test.snap @@ -52,7 +52,7 @@ }, "timestamp": "2025-07-04T12:35:18.703566" }, - "homo_sapiens - paired_end - stub": { + "arriba - homo_sapiens - paired_end": { "content": [ { "0": [ @@ -61,7 +61,7 @@ "id": "test", "single_end": false }, - "test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + "test.fusions.tsv:md5,7c3383f7eb6d79b84b0bd30a7ef02d70" ] ], "1": [ @@ -70,11 +70,11 @@ "id": "test", "single_end": false }, - "test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + "test.fusions.discarded.tsv:md5,445cb87a27f063e751f93498cf8d10b5" ] ], "2": [ - "versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" + "versions.yml:md5,d2eb9bb3bd4b21571a6aa2f39f1283af" ], "fusions": [ [ @@ -82,7 +82,7 @@ "id": "test", "single_end": false }, - "test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + "test.fusions.tsv:md5,7c3383f7eb6d79b84b0bd30a7ef02d70" ] ], "fusions_fail": [ @@ -91,18 +91,18 @@ "id": "test", "single_end": false }, - "test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + "test.fusions.discarded.tsv:md5,445cb87a27f063e751f93498cf8d10b5" ] ], "versions": [ - "versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" + "versions.yml:md5,d2eb9bb3bd4b21571a6aa2f39f1283af" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-10-08T15:41:23.945072" + "timestamp": "2025-07-22T14:12:04.304647041" } } \ No newline at end of file diff --git a/modules/nf-core/arriba/arriba/tests/nextflow.config b/modules/nf-core/arriba/arriba/tests/nextflow.config index d3d5b00f6..60aac1728 100644 --- a/modules/nf-core/arriba/arriba/tests/nextflow.config +++ b/modules/nf-core/arriba/arriba/tests/nextflow.config @@ -1,7 +1,8 @@ process { withName: STAR_GENOMEGENERATE { - ext.args = '--genomeSAindexNbases 11' + ext.args = '--genomeSAindexNbases 9' } + withName: STAR_ALIGN { ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50' } diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml index 81778a067..2a9284d7f 100644 --- a/modules/nf-core/cat/cat/meta.yml +++ b/modules/nf-core/cat/cat/meta.yml @@ -20,21 +20,24 @@ input: type: file description: List of compressed / uncompressed files pattern: "*" + ontologies: [] output: - - file_out: - - meta: - type: file - description: Concatenated file. Will be gzipped if file_out ends with ".gz" - pattern: "${file_out}" + file_out: + - - meta: + type: map + description: Groovy Map containing sample information - ${prefix}: type: file description: Concatenated file. Will be gzipped if file_out ends with ".gz" pattern: "${file_out}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@erikrikarddaniel" - "@FriederikeHanssen" diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index 91ff2fb5f..40d2f627c 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -21,9 +21,10 @@ input: type: file description: | List of input FastQ files to be concatenated. + ontologies: [] output: - - reads: - - meta: + reads: + - - meta: type: map description: | Groovy Map containing sample information @@ -32,11 +33,14 @@ output: type: file description: Merged fastq file pattern: "*.{merged.fastq.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 1342741d5..6e3e6c43a 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -48,7 +48,7 @@ process FASTP { $adapter_list \\ $fail_fastq \\ $args \\ - 2> >(tee ${prefix}.fastp.log >&2) \\ + 2>| >(tee ${prefix}.fastp.log >&2) \\ | gzip -c > ${prefix}.fastp.fastq.gz cat <<-END_VERSIONS > versions.yml @@ -69,7 +69,7 @@ process FASTP { $adapter_list \\ $fail_fastq \\ $args \\ - 2> >(tee ${prefix}.fastp.log >&2) + 2>| >(tee ${prefix}.fastp.log >&2) cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -94,7 +94,7 @@ process FASTP { --thread $task.cpus \\ --detect_adapter_for_pe \\ $args \\ - 2> >(tee ${prefix}.fastp.log >&2) + 2>| >(tee ${prefix}.fastp.log >&2) cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 9c4b24584..b8673272a 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -24,25 +24,27 @@ input: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. If you wish to run interleaved paired-end data, supply as single-end data but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. - - - adapter_fasta: - type: file - description: File in FASTA format containing possible adapters to remove. - pattern: "*.{fasta,fna,fas,fa}" - - - discard_trimmed_pass: - type: boolean - description: | - Specify true to not write any reads that pass trimming thresholds. - This can be used to use fastp for the output report only. - - - save_trimmed_fail: - type: boolean - description: Specify true to save files that failed to pass trimming thresholds - ending in `*.fail.fastq.gz` - - - save_merged: - type: boolean - description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` + ontologies: [] + - adapter_fasta: + type: file + description: File in FASTA format containing possible adapters to remove. + pattern: "*.{fasta,fna,fas,fa}" + ontologies: [] + - discard_trimmed_pass: + type: boolean + description: | + Specify true to not write any reads that pass trimming thresholds. + This can be used to use fastp for the output report only. + - save_trimmed_fail: + type: boolean + description: Specify true to save files that failed to pass trimming thresholds + ending in `*.fail.fastq.gz` + - save_merged: + type: boolean + description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` output: - - reads: - - meta: + reads: + - - meta: type: map description: | Groovy Map containing sample information @@ -51,8 +53,10 @@ output: type: file description: The trimmed/modified/unmerged fastq reads pattern: "*fastp.fastq.gz" - - json: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + json: + - - meta: type: map description: | Groovy Map containing sample information @@ -61,8 +65,10 @@ output: type: file description: Results in JSON format pattern: "*.json" - - html: - - meta: + ontologies: + - edam: http://edamontology.org/format_3464 # JSON + html: + - - meta: type: map description: | Groovy Map containing sample information @@ -71,8 +77,9 @@ output: type: file description: Results in HTML format pattern: "*.html" - - log: - - meta: + ontologies: [] + log: + - - meta: type: map description: | Groovy Map containing sample information @@ -81,8 +88,9 @@ output: type: file description: fastq log file pattern: "*.log" - - reads_fail: - - meta: + ontologies: [] + reads_fail: + - - meta: type: map description: | Groovy Map containing sample information @@ -91,8 +99,10 @@ output: type: file description: Reads the failed the preprocessing pattern: "*fail.fastq.gz" - - reads_merged: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + reads_merged: + - - meta: type: map description: | Groovy Map containing sample information @@ -101,11 +111,14 @@ output: type: file description: Reads that were successfully merged pattern: "*.{merged.fastq.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 89960e04c..21e668c09 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -1,11 +1,11 @@ process GATK4_BEDTOINTERVALLIST { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': - 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd'}" input: tuple val(meta), path(bed) @@ -13,7 +13,7 @@ process GATK4_BEDTOINTERVALLIST { output: tuple val(meta), path('*.interval_list'), emit: interval_list - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -24,18 +24,19 @@ process GATK4_BEDTOINTERVALLIST { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK BedToIntervalList] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK BedToIntervalList] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ BedToIntervalList \\ - --INPUT $bed \\ + --INPUT ${bed} \\ --OUTPUT ${prefix}.interval_list \\ - --SEQUENCE_DICTIONARY $dict \\ + --SEQUENCE_DICTIONARY ${dict} \\ --TMP_DIR . \\ - $args + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/bedtointervallist/meta.yml b/modules/nf-core/gatk4/bedtointervallist/meta.yml index 25348e162..b186132d0 100644 --- a/modules/nf-core/gatk4/bedtointervallist/meta.yml +++ b/modules/nf-core/gatk4/bedtointervallist/meta.yml @@ -26,6 +26,7 @@ input: type: file description: Input bed file pattern: "*.bed" + ontologies: [] - - meta2: type: map description: | @@ -35,25 +36,26 @@ input: type: file description: Sequence dictionary pattern: "*.dict" + ontologies: [] output: - - interval_list: - - meta: + interval_list: + - - meta: type: file description: gatk interval list file pattern: "*.interval_list" + ontologies: [] - "*.interval_list": type: file description: gatk interval list file pattern: "*.interval_list" - - _list: - type: file - description: gatk interval list file - pattern: "*.interval_list" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 998622a06..872648a5e 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -1,18 +1,18 @@ process GATK4_CREATESEQUENCEDICTIONARY { - tag "$fasta" + tag "${fasta}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': - 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd'}" input: tuple val(meta), path(fasta) output: - tuple val(meta), path('*.dict') , emit: dict - path "versions.yml" , emit: versions + tuple val(meta), path('*.dict'), emit: dict + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -22,17 +22,18 @@ process GATK4_CREATESEQUENCEDICTIONARY { def avail_mem = 6144 if (!task.memory) { - log.info '[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ CreateSequenceDictionary \\ - --REFERENCE $fasta \\ - --URI $fasta \\ + --REFERENCE ${fasta} \\ + --URI ${fasta} \\ --TMP_DIR . \\ - $args + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index 7b5156bb3..72dced28c 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -26,21 +26,26 @@ input: type: file description: Input fasta file pattern: "*.{fasta,fa}" + ontologies: [] output: - - dict: - - meta: + dict: + - - meta: type: file description: gatk dictionary file pattern: "*.{dict}" + ontologies: [] - "*.dict": type: file description: gatk dictionary file pattern: "*.{dict}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@maxulysse" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index f4bd896bf..5fb161b4f 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -13,12 +13,12 @@ process GATK4_MARKDUPLICATES { path fasta_fai output: - tuple val(meta), path("*cram"), emit: cram, optional: true - tuple val(meta), path("*bam"), emit: bam, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.bai"), emit: bai, optional: true + tuple val(meta), path("*cram"), emit: cram, optional: true + tuple val(meta), path("*bam"), emit: bam, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.bai"), emit: bai, optional: true tuple val(meta), path("*.metrics"), emit: metrics - 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/markduplicates/meta.yml b/modules/nf-core/gatk4/markduplicates/meta.yml index 4772c5f39..335c309a9 100644 --- a/modules/nf-core/gatk4/markduplicates/meta.yml +++ b/modules/nf-core/gatk4/markduplicates/meta.yml @@ -28,17 +28,20 @@ input: type: file description: Sorted BAM file pattern: "*.{bam}" - - - fasta: - type: file - description: Fasta file - pattern: "*.{fasta}" - - - fasta_fai: - type: file - description: Fasta index file - pattern: "*.{fai}" + ontologies: [] + - fasta: + type: file + description: Fasta file + pattern: "*.{fasta}" + ontologies: [] + - fasta_fai: + type: file + description: Fasta index file + pattern: "*.{fai}" + ontologies: [] output: - - cram: - - meta: + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -47,8 +50,9 @@ output: type: file description: Marked duplicates CRAM file pattern: "*.{cram}" - - bam: - - meta: + ontologies: [] + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -57,8 +61,9 @@ output: type: file description: Marked duplicates BAM file pattern: "*.{bam}" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -67,8 +72,9 @@ output: type: file description: CRAM index file pattern: "*.{cram.crai}" - - bai: - - meta: + ontologies: [] + bai: + - - meta: type: map description: | Groovy Map containing sample information @@ -77,8 +83,9 @@ output: type: file description: BAM index file pattern: "*.{bam.bai}" - - metrics: - - meta: + ontologies: [] + metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -87,11 +94,14 @@ output: type: file description: Duplicate metrics file generated by GATK pattern: "*.{metrics.txt}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@ajodeh-juma" - "@FriederikeHanssen" diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml index bebe7f575..715efec8e 100644 --- a/modules/nf-core/gffread/meta.yml +++ b/modules/nf-core/gffread/meta.yml @@ -25,35 +25,39 @@ input: type: file description: A reference file in either the GFF3, GFF2 or GTF format. pattern: "*.{gff, gtf}" - - - fasta: - type: file - description: A multi-fasta file with the genomic sequences - pattern: "*.{fasta,fa,faa,fas,fsa}" + ontologies: [] + - fasta: + type: file + description: A multi-fasta file with the genomic sequences + pattern: "*.{fasta,fa,faa,fas,fsa}" + ontologies: [] output: - - gtf: - - meta: + gtf: + - - meta: type: map description: | Groovy Map containing meta data e.g. [ id:'test' ] - "*.gtf": type: file - description: GTF file resulting from the conversion of the GFF input file if - '-T' argument is present + description: GTF file resulting from the conversion of the GFF input file + if '-T' argument is present pattern: "*.{gtf}" - - gffread_gff: - - meta: + ontologies: [] + gffread_gff: + - - meta: type: map description: | Groovy Map containing meta data e.g. [ id:'test' ] - "*.gff3": type: file - description: GFF3 file resulting from the conversion of the GFF input file if - '-T' argument is absent + description: GFF3 file resulting from the conversion of the GFF input file + if '-T' argument is absent pattern: "*.gff3" - - gffread_fasta: - - meta: + ontologies: [] + gffread_fasta: + - - meta: type: map description: | Groovy Map containing meta data @@ -63,11 +67,14 @@ output: description: Fasta file produced when either of '-w', '-x', '-y' parameters is present pattern: "*.fasta" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 812fc4c5e..f89370483 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.29 + - bioconda::multiqc=1.30 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 0ac3c3699..67460de9a 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' : - 'biocontainers/multiqc:1.29--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.30--pyhdfd78af_1' : + 'biocontainers/multiqc:1.30--pyhdfd78af_1' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 88e90571c..0d3f288bd 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,e65ce731db2128b8e4dd43d6e880fc1c" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-22T11:50:41.182332996" + "timestamp": "2025-07-10T08:06:23.563041241" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,e65ce731db2128b8e4dd43d6e880fc1c" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-22T11:51:22.448739369" + "timestamp": "2025-07-10T08:06:48.96226832" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,e65ce731db2128b8e4dd43d6e880fc1c" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-22T11:51:06.198928424" + "timestamp": "2025-07-10T08:06:40.627008706" } -} \ No newline at end of file +} diff --git a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml index 0947048dc..1c4572c58 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml +++ b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml @@ -24,9 +24,10 @@ input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + ontologies: [] output: - - metrics: - - meta: + metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -35,8 +36,9 @@ output: type: file description: Values used by Picard to generate the insert size histograms pattern: "*.txt" - - histogram: - - meta: + ontologies: [] + histogram: + - - meta: type: map description: | Groovy Map containing sample information @@ -45,11 +47,14 @@ output: type: file description: Insert size histogram in PDF format pattern: "*.pdf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@FerriolCalvet" maintainers: diff --git a/modules/nf-core/picard/collectrnaseqmetrics/meta.yml b/modules/nf-core/picard/collectrnaseqmetrics/meta.yml index 15d146baa..b8da63e9f 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/meta.yml +++ b/modules/nf-core/picard/collectrnaseqmetrics/meta.yml @@ -27,18 +27,22 @@ input: type: file description: BAM/SAM file pattern: "*.{bam,sam}" - - - ref_flat: - type: file - description: Genome ref_flat file - - - fasta: - type: file - description: Genome fasta file - - - rrna_intervals: - type: file - description: Interval file of ribosomal RNA regions + ontologies: [] + - ref_flat: + type: file + description: Genome ref_flat file + ontologies: [] + - fasta: + type: file + description: Genome fasta file + ontologies: [] + - rrna_intervals: + type: file + description: Interval file of ribosomal RNA regions + ontologies: [] output: - - metrics: - - meta: + metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -47,21 +51,25 @@ output: type: file description: RNA alignment metrics files generated by picard pattern: "*.rna_metrics" - - pdf: - - meta: + ontologies: [] + pdf: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - "*.pdf": type: file - description: Plot normalized position vs. coverage in a pdf file generated by - picard - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + description: Plot normalized position vs. coverage in a pdf file generated + by picard + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index bb7480809..a27e0a88c 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -26,10 +26,12 @@ input: type: file description: Aligned reads file pattern: "*.{bam, cram}" + ontologies: [] - bai: type: file description: (Optional) Aligned reads file index pattern: "*.{bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -39,6 +41,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta,fna}" + ontologies: [] - - meta3: type: map description: | @@ -48,13 +51,15 @@ input: type: file description: Genome fasta file index pattern: "*.{fai}" - - - intervallist: - type: file - description: Picard Interval List. Defines which contigs to include. Can be - generated from a BED file with GATK BedToIntervalList. + ontologies: [] + - intervallist: + type: file + description: Picard Interval List. Defines which contigs to include. Can be generated + from a BED file with GATK BedToIntervalList. + ontologies: [] output: - - metrics: - - meta: + metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -63,11 +68,14 @@ output: type: file description: Alignment metrics files generated by picard pattern: "*_{metrics}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@flowuenne" diff --git a/modules/nf-core/salmon/index/meta.yml b/modules/nf-core/salmon/index/meta.yml index 48486a2bb..4e0367b4a 100644 --- a/modules/nf-core/salmon/index/meta.yml +++ b/modules/nf-core/salmon/index/meta.yml @@ -15,23 +15,27 @@ tools: licence: ["GPL-3.0-or-later"] identifier: biotools:salmon input: - - - genome_fasta: - type: file - description: Fasta file of the reference genome - - - transcript_fasta: - type: file - description: Fasta file of the reference transcriptome + - genome_fasta: + type: file + description: Fasta file of the reference genome + ontologies: [] + - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome + ontologies: [] output: - - index: - - salmon: - type: directory - description: Folder containing the star index files - pattern: "salmon" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + index: + - salmon: + type: directory + description: Folder containing the star index files + pattern: "salmon" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/salmon/quant/meta.yml b/modules/nf-core/salmon/quant/meta.yml index 4cacde0f0..40e8eb965 100644 --- a/modules/nf-core/salmon/quant/meta.yml +++ b/modules/nf-core/salmon/quant/meta.yml @@ -26,25 +26,28 @@ input: List of input FastQ files for single-end or paired-end data. Multiple single-end fastqs or pairs of paired-end fastqs are handled. - - - index: - type: directory - description: Folder containing the star index files - - - gtf: - type: file - description: GTF of the reference transcriptome - - - transcript_fasta: - type: file - description: Fasta file of the reference transcriptome - - - alignment_mode: - type: boolean - description: whether to run salmon in alignment mode - - - lib_type: - type: string - description: | - Override library type inferred based on strandedness defined in meta object + ontologies: [] + - index: + type: directory + description: Folder containing the star index files + - gtf: + type: file + description: GTF of the reference transcriptome + ontologies: [] + - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome + ontologies: [] + - alignment_mode: + type: boolean + description: whether to run salmon in alignment mode + - lib_type: + type: string + description: | + Override library type inferred based on strandedness defined in meta object output: - - results: - - meta: + results: + - - meta: type: directory description: Folder containing the quantification results for a specific sample pattern: "${prefix}" @@ -52,30 +55,35 @@ output: type: directory description: Folder containing the quantification results for a specific sample pattern: "${prefix}" - - json_info: - - meta: - type: file - description: File containing meta information from Salmon quant - pattern: "*info.json" + json_info: + - - meta: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" - "*info.json": type: file description: File containing meta information from Salmon quant pattern: "*info.json" - - lib_format_counts: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + ontologies: + - edam: http://edamontology.org/format_3464 # JSON + lib_format_counts: + - - meta: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" - "*lib_format_counts.json": type: file description: File containing the library format counts pattern: "*lib_format_counts.json" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3464 # JSON + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/samtools/convert/meta.yml b/modules/nf-core/samtools/convert/meta.yml index d5bfa161b..519812ab5 100644 --- a/modules/nf-core/samtools/convert/meta.yml +++ b/modules/nf-core/samtools/convert/meta.yml @@ -26,10 +26,12 @@ input: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" + ontologies: [] - index: type: file description: BAM/CRAM index file pattern: "*.{bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -39,6 +41,7 @@ input: type: file description: Reference file to create the CRAM file pattern: "*.{fasta,fa}" + ontologies: [] - - meta3: type: map description: | @@ -48,9 +51,10 @@ input: type: file description: Reference index file to create the CRAM file pattern: "*.{fai}" + ontologies: [] output: - - bam: - - meta: + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -59,8 +63,9 @@ output: type: file description: filtered/converted BAM file pattern: "*{.bam}" - - cram: - - meta: + ontologies: [] + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -69,8 +74,9 @@ output: type: file description: filtered/converted CRAM file pattern: "*{cram}" - - bai: - - meta: + ontologies: [] + bai: + - - meta: type: map description: | Groovy Map containing sample information @@ -79,8 +85,9 @@ output: type: file description: filtered/converted BAM index pattern: "*{.bai}" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -89,11 +96,14 @@ output: type: file description: filtered/converted CRAM index pattern: "*{.crai}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@FriederikeHanssen" - "@maxulysse" diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 256a330a1..b7a2e0c1a 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -26,6 +26,7 @@ input: type: file description: FASTA file pattern: "*.{fa,fasta}" + ontologies: [] - - meta2: type: map description: | @@ -35,13 +36,14 @@ input: type: file description: FASTA index file pattern: "*.{fai}" - - - get_sizes: - type: boolean - description: use cut to get the sizes of the index (true) or not (false) + ontologies: [] + - get_sizes: + type: boolean + description: use cut to get the sizes of the index (true) or not (false) output: - - fa: - - meta: + fa: + - - meta: type: map description: | Groovy Map containing sample information @@ -50,28 +52,31 @@ output: type: file description: FASTA file pattern: "*.{fa}" - - fai: - - meta: + ontologies: [] + sizes: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.fai": + - "*.sizes": type: file - description: FASTA index file - pattern: "*.{fai}" - - sizes: - - meta: + description: File containing chromosome lengths + pattern: "*.{sizes}" + ontologies: [] + fai: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.sizes": + - "*.fai": type: file - description: File containing chromosome lengths - pattern: "*.{sizes}" - - gzi: - - meta: + description: FASTA index file + pattern: "*.{fai}" + ontologies: [] + gzi: + - - meta: type: map description: | Groovy Map containing sample information @@ -80,11 +85,14 @@ output: type: file description: Optional gzip index file for compressed inputs pattern: "*.gzi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 311756102..7019a72e4 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -24,7 +24,7 @@ process SAMTOOLS_INDEX { """ samtools \\ index \\ - -@ ${task.cpus-1} \\ + -@ ${task.cpus} \\ $args \\ $input diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index db8df0d50..1bed6bca6 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -25,9 +25,10 @@ input: - input: type: file description: input file + ontologies: [] output: - - bai: - - meta: + bai: + - - meta: type: map description: | Groovy Map containing sample information @@ -36,8 +37,9 @@ output: type: file description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -46,8 +48,9 @@ output: type: file description: CSI index file pattern: "*.{csi}" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -56,11 +59,14 @@ output: type: file description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index 5cfe763e3..1ee469052 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -26,6 +26,7 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: [] - - meta2: type: map description: | @@ -44,18 +45,19 @@ input: type: file description: Annotation GTF file pattern: "*.{gtf}" - - - star_ignore_sjdbgtf: - type: boolean - description: Ignore annotation GTF file - - - seq_platform: - type: string - description: Sequencing platform - - - seq_center: - type: string - description: Sequencing center + ontologies: [] + - star_ignore_sjdbgtf: + type: boolean + description: Ignore annotation GTF file + - seq_platform: + type: string + description: Sequencing platform + - seq_center: + type: string + description: Sequencing center output: - - log_final: - - meta: + log_final: + - - meta: type: map description: | Groovy Map containing sample information @@ -64,8 +66,9 @@ output: type: file description: STAR final log file pattern: "*Log.final.out" - - log_out: - - meta: + ontologies: [] + log_out: + - - meta: type: map description: | Groovy Map containing sample information @@ -74,8 +77,9 @@ output: type: file description: STAR lot out file pattern: "*Log.out" - - log_progress: - - meta: + ontologies: [] + log_progress: + - - meta: type: map description: | Groovy Map containing sample information @@ -84,13 +88,16 @@ output: type: file description: STAR log progress file pattern: "*Log.progress.out" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - - meta: + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -99,8 +106,9 @@ output: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - - bam_sorted: - - meta: + ontologies: [] + bam_sorted: + - - meta: type: map description: | Groovy Map containing sample information @@ -109,8 +117,9 @@ output: type: file description: Sorted BAM file of read alignments (optional) pattern: "*sortedByCoord.out.bam" - - bam_sorted_aligned: - - meta: + ontologies: [] + bam_sorted_aligned: + - - meta: type: map description: | Groovy Map containing sample information @@ -119,8 +128,9 @@ output: type: file description: Sorted BAM file of read alignments (optional) pattern: "*.Aligned.sortedByCoord.out.bam" - - bam_transcript: - - meta: + ontologies: [] + bam_transcript: + - - meta: type: map description: | Groovy Map containing sample information @@ -129,8 +139,9 @@ output: type: file description: Output BAM file of transcriptome alignment (optional) pattern: "*toTranscriptome.out.bam" - - bam_unsorted: - - meta: + ontologies: [] + bam_unsorted: + - - meta: type: map description: | Groovy Map containing sample information @@ -139,8 +150,9 @@ output: type: file description: Unsorted BAM file of read alignments (optional) pattern: "*Aligned.unsort.out.bam" - - fastq: - - meta: + ontologies: [] + fastq: + - - meta: type: map description: | Groovy Map containing sample information @@ -149,8 +161,10 @@ output: type: file description: Unmapped FastQ files (optional) pattern: "*fastq.gz" - - tab: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + tab: + - - meta: type: map description: | Groovy Map containing sample information @@ -159,8 +173,10 @@ output: type: file description: STAR output tab file(s) (optional) pattern: "*.tab" - - spl_junc_tab: - - meta: + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + spl_junc_tab: + - - meta: type: map description: | Groovy Map containing sample information @@ -169,8 +185,10 @@ output: type: file description: STAR output splice junction tab file pattern: "*.SJ.out.tab" - - read_per_gene_tab: - - meta: + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + read_per_gene_tab: + - - meta: type: map description: | Groovy Map containing sample information @@ -179,8 +197,10 @@ output: type: file description: STAR output read per gene tab file pattern: "*.ReadsPerGene.out.tab" - - junction: - - meta: + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + junction: + - - meta: type: map description: | Groovy Map containing sample information @@ -189,19 +209,20 @@ output: type: file description: STAR chimeric junction output file (optional) pattern: "*.out.junction" - - sam: - - meta: + ontologies: [] + sam: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*.out.sam" - "*.out.sam": type: file description: STAR output SAM file(s) (optional) pattern: "*.out.sam" - - wig: - - meta: + ontologies: [] + wig: + - - meta: type: map description: | Groovy Map containing sample information @@ -210,8 +231,9 @@ output: type: file description: STAR output wiggle format file(s) (optional) pattern: "*.wig" - - bedgraph: - - meta: + ontologies: [] + bedgraph: + - - meta: type: map description: | Groovy Map containing sample information @@ -220,6 +242,7 @@ output: type: file description: STAR output bedGraph format file(s) (optional) pattern: "*.bg" + ontologies: [] authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index 33c1f65f3..39ed3cbde 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -24,6 +24,7 @@ input: - fasta: type: file description: Fasta file of the reference genome + ontologies: [] - - meta2: type: map description: | @@ -32,9 +33,10 @@ input: - gtf: type: file description: GTF file of the reference genome + ontologies: [] output: - - index: - - meta: + index: + - - meta: type: map description: | Groovy Map containing sample information @@ -43,11 +45,13 @@ output: type: directory description: Folder containing the star index files pattern: "star" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/starfusion/build/tests/main.nf.test b/modules/nf-core/starfusion/build/tests/main.nf.test index ae18299e2..2fa9f044c 100644 --- a/modules/nf-core/starfusion/build/tests/main.nf.test +++ b/modules/nf-core/starfusion/build/tests/main.nf.test @@ -23,13 +23,13 @@ nextflow_process { input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/CTAT_HumanFusionLib.mini.dat.gz') input[3] = "homo_sapiens" - input[4] = "http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam37.4/Pfam-A.hmm.gz" + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/Pfam-A.hmm.gz') input[5] = [ - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3f", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3i", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3p" + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3f'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3i'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3m'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3p') ] input[6] = "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm" """ @@ -125,22 +125,22 @@ nextflow_process { """ input[0] = [ [ id:'minigenome_fasta' ], - file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.fa") + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/minigenome.fa') ] input[1] = [ [ id:'minigenome_gtf' ], - file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.gtf") + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/minigenome.gtf') ] - input[2] = file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz") + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/CTAT_HumanFusionLib.mini.dat.gz') input[3] = "homo_sapiens" - input[4] = "http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam37.4/Pfam-A.hmm.gz" + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/Pfam-A.hmm.gz') input[5] = [ - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3f", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3i", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3p" + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3f'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3i'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3m'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3p') ] input[6] = "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm" """ @@ -160,21 +160,21 @@ nextflow_process { """ input[0] = [ [ id:'minigenome_fasta' ], - file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.fa") + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/minigenome.fa') ] input[1] = [ [ id:'minigenome_gtf' ], - file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.gtf") + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/minigenome.gtf') ] - input[2] = file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz") + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/CTAT_HumanFusionLib.mini.dat.gz') input[3] = "homo_sapiens" - input[4] = "http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam37.4/Pfam-A.hmm.gz" + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/Pfam-A.hmm.gz') input[5] = [ - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3f", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3i", - "https://www.dfam.org/releases/Dfam_3.8/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m" + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3f'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3i'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/test_starfusion_dfam.hmm.h3m') ] input[6] = "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm" """ diff --git a/modules/nf-core/stringtie/merge/meta.yml b/modules/nf-core/stringtie/merge/meta.yml index cf6902b32..3201746c2 100644 --- a/modules/nf-core/stringtie/merge/meta.yml +++ b/modules/nf-core/stringtie/merge/meta.yml @@ -13,27 +13,32 @@ tools: licence: ["MIT"] identifier: biotools:stringtie input: - - - stringtie_gtf: + - stringtie_gtf: + type: file + description: | + Stringtie transcript gtf output(s). + pattern: "*.gtf" + ontologies: [] + - annotation_gtf: + type: file + description: | + Annotation gtf file (optional). + pattern: "*.gtf" + ontologies: [] +output: + gtf: + - stringtie.merged.gtf: type: file - description: | - Stringtie transcript gtf output(s). - pattern: "*.gtf" - - - annotation_gtf: + description: Merged gtf file + pattern: "stringtie.merged.gtf" + ontologies: [] + versions: + - versions.yml: type: file - description: | - Annotation gtf file (optional). - pattern: "*.gtf" -output: - - gtf: - - stringtie.merged.gtf: - type: file - description: Merged gtf file - pattern: "stringtie.merged.gtf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@yuukiiwa" maintainers: diff --git a/modules/nf-core/stringtie/stringtie/meta.yml b/modules/nf-core/stringtie/stringtie/meta.yml index e55b2abfc..9cdd14004 100644 --- a/modules/nf-core/stringtie/stringtie/meta.yml +++ b/modules/nf-core/stringtie/stringtie/meta.yml @@ -23,13 +23,15 @@ input: type: file description: | Stringtie transcript gtf output(s). - - - annotation_gtf: - type: file - description: | - Annotation gtf file (optional). + ontologies: [] + - annotation_gtf: + type: file + description: | + Annotation gtf file (optional). + ontologies: [] output: - - transcript_gtf: - - meta: + transcript_gtf: + - - meta: type: map description: | Groovy Map containing sample information @@ -38,8 +40,9 @@ output: type: file description: transcript gtf pattern: "*.{transcripts.gtf}" - - abundance: - - meta: + ontologies: [] + abundance: + - - meta: type: map description: | Groovy Map containing sample information @@ -48,8 +51,9 @@ output: type: file description: abundance pattern: "*.{abundance.txt}" - - coverage_gtf: - - meta: + ontologies: [] + coverage_gtf: + - - meta: type: map description: | Groovy Map containing sample information @@ -58,8 +62,9 @@ output: type: file description: coverage gtf pattern: "*.{coverage.gtf}" - - ballgown: - - meta: + ontologies: [] + ballgown: + - - meta: type: map description: | Groovy Map containing sample information @@ -68,11 +73,14 @@ output: type: file description: for running ballgown pattern: "*.{ballgown}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/gtftogenepred/meta.yml b/modules/nf-core/ucsc/gtftogenepred/meta.yml index cf04154d4..5939538df 100644 --- a/modules/nf-core/ucsc/gtftogenepred/meta.yml +++ b/modules/nf-core/ucsc/gtftogenepred/meta.yml @@ -22,9 +22,10 @@ input: type: file description: GTF file pattern: "*.{gtf}" + ontologies: [] output: - - genepred: - - meta: + genepred: + - - meta: type: map description: | Groovy Map containing sample information @@ -33,8 +34,9 @@ output: type: file description: genepred file pattern: "*.{genepred}" - - refflat: - - meta: + ontologies: [] + refflat: + - - meta: type: map description: | Groovy Map containing sample information @@ -43,11 +45,14 @@ output: type: file description: refflat file pattern: "*.{refflat}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@BarryDigby" - "@anoronh4" diff --git a/nextflow.config b/nextflow.config index ef54ad4e6..bf0f24ca1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -301,23 +301,46 @@ dag { manifest { name = 'nf-core/rnafusion' contributors = [ - // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ name: 'Martin Proks', affiliation: '', email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + github: '@matq007', + contribution: ['author'], orcid: '' ], [ - name: ' Annick Renevey', - affiliation: '', + name: 'Annick Renevey', + affiliation: 'SciLifeLab, Karolinska Institutet', + email: 'annick.renevey@scilifelab.se', + github: '@rannick', + contribution: ['author', 'maintainer'], + orcid: '0000-0001-7411-6063' + ], + [ + name: 'Maxime U Garcia', + affiliation: 'Seqera', + email: 'maxime.garcia@seqera.io', + github: '@maxulysse', + contribution: ['author'], + orcid: '0000-0003-2827-9261' + ], + [ + name: 'Anabella Trigila', + affiliation: 'ZS Associates', email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + github: '@atrigila', + contribution: ['contributor', 'maintainer'], orcid: '' ], + [ + name: 'Nicolas Vannieuwkerke', + affiliation: 'Center for Medical Genetics Ghent', + email: '', + github: '@nvnieuwk', + contribution: ['contributor', 'maintainer'], + orcid: '' + ] ] homePage = 'https://github.com/nf-core/rnafusion' description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" diff --git a/nextflow_schema.json b/nextflow_schema.json index 5b15693b1..b6ce64d69 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -39,6 +39,7 @@ "input": { "type": "string", "format": "file-path", + "mimetype": "text/csv", "schema": "assets/schema_input.json", "exists": true, "pattern": "^\\S+\\.(csv|yaml|yml|json)$", @@ -335,16 +336,19 @@ }, "save_trimmed_fail": { "type": "boolean", - "fa_icon": "far fa-times-circle" + "fa_icon": "far fa-times-circle", + "description": "FASTP: Specify true to save files that failed to pass trimming thresholds" }, "min_trimmed_reads": { "type": "integer", "default": 1, - "fa_icon": "fas fa-search-minus" + "fa_icon": "fas fa-search-minus", + "description": "FASTP: Inputs with fewer than this reads will be filtered out of the \"reads\" output channel" }, "save_merged": { "type": "boolean", - "fa_icon": "fas fa-download" + "fa_icon": "fas fa-download", + "description": "FASTP: Specify true to save merged reads" } } }, diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 3925e8228..bcd77eb1e 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2025-07-08T11:39:11+00:00", - "description": "

\n \n \n \"nf-core/rnafusion\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnafusion)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnafusion-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnafusion)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from up to 3 fusion callers tools are created, and are also aggregated, most notably in a pdf visualisation document, a vcf data collection file, and html and tsv reports.\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results).\n\nIn rnafusion the full-sized test includes reference building and fusion detection. The test dataset is taken from [here](https://github.com/nf-core/test-datasets/tree/rnafusion/testdata/human).\n\n## Pipeline summary\n\n![nf-core/rnafusion metro map](docs/images/nf-core-rnafusion_metro_map.png)\n\n### References\n\nThe references for the pipeline can be downloaded from the nf-core AWS megatests S3 bucket using the following command for the [AWS CLI tool](https://github.com/aws/aws-cli):\n\n```bash\naws --no-sign-request s3 sync s3://nf-core-awsmegatests/rnafusion/references/ \n```\n\nThe path to the downloaded references can then be provided to the pipeline with the `--genomes_base` parameter.\n\n\u26a0\ufe0f **Please note that the references are large and can take a long time to download, so it is recommended to download them once and use them for all future runs of the pipeline.**\n\nThe pipeline is also able to build the references in case files from a specific gencode version are missing (Note: only gencode 46 is available for fusioncatcher). This is done automatically when the expected references are not found and these files will be automatically published in the directory specified by the `--genomes_base` parameter. Use the `--references_only` parameter to trigger the reference building workflow only, without running the rest of the pipeline.\n\n1. Download gencode fasta and gtf files\n2. Download the HGNC nomenclature file\n3. Create files needed for QC (Sequence Dictionary and RRNA intervals)\n4. Convert the gtf file to a refflat file\n5. Create the [Salmon](https://salmon.readthedocs.io/en/latest/) index\n6. Create [STAR](https://github.com/alexdobin/STAR) index\n7. Build [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) and [CTAT-SPLICING](https://github.com/TrinityCTAT/CTAT-SPLICING) references\n8. Download [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) DBs\n\n> [!WARNING]\n> References for Fusioncatcher and Arriba cannot be automatically created by the pipeline and should be downloaded from the S3 bucket or another source. See the [References](#references) section for more information.\n\n#### Main workflow\n\n1. Input samplesheet check\n2. Reads quality control ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Optional trimming with [fastp](https://github.com/OpenGene/fastp)\n4. Align FASTQs to BAM with [STAR](https://github.com/alexdobin/STAR)\n5. Run fusion detection with [Arriba](https://github.com/suhrig/arriba)\n6. Run fusion detection with [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion)\n 7a. Optional trimming of 3' end with [fastp](https://github.com/OpenGene/fastp) to feed into fusioncatcher (other tools not affected)\n 7b. Run fusion detection with [FusionCatcher](https://github.com/ndaniel/fusioncatcher)\n7. Run transcript assembly and quantification with [StringTie](https://ccb.jhu.edu/software/stringtie/)\n8. Run cancer splicing aberrations detection with [CTAT-SPLICING](https://github.com/TrinityCTAT/CTAT-SPLICING)\n9. Merge all fusions detected by the selected tools with [Fusion-report](https://github.com/Clinical-Genomics/fusion-report)\n10. Post-processing and analysis of data\n - [FusionInspector](https://github.com/FusionInspector/FusionInspector)\n - Summarize information into a VCF file\n - [Arriba](https://github.com/suhrig/arriba) visualisation\n - Collect metrics ([`picard CollectRnaSeqMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037057492-CollectRnaSeqMetrics-Picard-)), [`picard CollectInsertSizeMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037055772-CollectInsertSizeMetrics-Picard-) and ([`GATK MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-))\n11. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n12. Compress bam files to cram with [samtools view](http://www.htslib.org/)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nAs the reference building is computationally heavy (> 24h on HPC), we had to use dummy reference files in the test profile. Therefore, it is recommended to run the test profile with the `-stub` option.\n\n```bash\nnextflow run nf-core/rnafusion \\\n -profile test, \\\n --outdir \\\n -stub\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n> **Notes:**\n>\n> - Conda is not currently supported; run with singularity or docker.\n> - Paths need to be absolute.\n> - GRCh38 is the only supported reference.\n> - Single-end reads are to be used as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp.\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnafusion/usage) and the [parameter documentation](https://nf-co.re/rnafusion/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnafusion/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnafusion/output).\n\n## Credits\n\nnf-core/rnafusion was written by Martin Proks ([@matq007](https://github.com/matq007)), Maxime Garcia ([@maxulysse](https://github.com/maxulysse)) and Annick Renevey ([@rannick](https://github.com/rannick))\n\n## We thank the following people for their help in the development of this pipeline\n\n- [Phil Ewels](https://github.com/ewels)\n- [Rickard Hammar\u00e9n](https://github.com/Hammarn)\n- [Alexander Peltzer](https://github.com/apeltzer)\n- [Praveen Raj](https://github.com/praveenraj2018)\n- [Anabella Trigila](https://github.com/atrigila)\n- [Nicolas Vannieuwkerke](https://github.com/nvnieuwk)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnafusion` channel](https://nfcore.slack.com/channels/rnafusion) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/rnafusion for your analysis, please cite it using the following doi: [10.5281/zenodo.3946477](https://doi.org/10.5281/zenodo.3946477)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "description": "

\n \n \n \"nf-core/rnafusion\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.2565517-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.2565517)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnafusion)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnafusion-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnafusion)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from up to 3 fusion callers tools are created, and are also aggregated, most notably in a pdf visualisation document, a vcf data collection file, and html and tsv reports.\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results).\n\nIn rnafusion the full-sized test includes reference building and fusion detection. The test dataset is taken from [here](https://github.com/nf-core/test-datasets/tree/rnafusion/testdata/human).\n\n## Pipeline summary\n\n![nf-core/rnafusion metro map](docs/images/nf-core-rnafusion_metro_map.png)\n\n### References\n\nThe references for the pipeline can be downloaded from the nf-core AWS megatests S3 bucket using the following command for the [AWS CLI tool](https://github.com/aws/aws-cli):\n\n```bash\naws --no-sign-request s3 sync s3://nf-core-awsmegatests/rnafusion/references/ \n```\n\nThe path to the downloaded references can then be provided to the pipeline with the `--genomes_base` parameter.\n\n\u26a0\ufe0f **Please note that the references are large and can take a long time to download, so it is recommended to download them once and use them for all future runs of the pipeline.**\n\nThe pipeline is also able to build the references in case files from a specific gencode version are missing (Note: only gencode 46 is available for fusioncatcher). This is done automatically when the expected references are not found and these files will be automatically published in the directory specified by the `--genomes_base` parameter. Use the `--references_only` parameter to trigger the reference building workflow only, without running the rest of the pipeline.\n\n1. Download gencode fasta and gtf files\n2. Download the HGNC nomenclature file\n3. Create files needed for QC (Sequence Dictionary and RRNA intervals)\n4. Convert the gtf file to a refflat file\n5. Create the [Salmon](https://salmon.readthedocs.io/en/latest/) index\n6. Create [STAR](https://github.com/alexdobin/STAR) index\n7. Build [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) and [CTAT-SPLICING](https://github.com/TrinityCTAT/CTAT-SPLICING) references\n8. Download [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) DBs\n\n> [!WARNING]\n> References for Fusioncatcher and Arriba cannot be automatically created by the pipeline and should be downloaded from the S3 bucket or another source. See the [References](#references) section for more information.\n\n#### Main workflow\n\n1. Input samplesheet check\n2. Reads quality control ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Optional trimming with [fastp](https://github.com/OpenGene/fastp)\n4. Align FASTQs to BAM with [STAR](https://github.com/alexdobin/STAR)\n5. Run fusion detection with [Arriba](https://github.com/suhrig/arriba)\n6. Run fusion detection with [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion)\n 7a. Optional trimming of 3' end with [fastp](https://github.com/OpenGene/fastp) to feed into fusioncatcher (other tools not affected)\n 7b. Run fusion detection with [FusionCatcher](https://github.com/ndaniel/fusioncatcher)\n7. Run transcript assembly and quantification with [StringTie](https://ccb.jhu.edu/software/stringtie/)\n8. Run cancer splicing aberrations detection with [CTAT-SPLICING](https://github.com/TrinityCTAT/CTAT-SPLICING)\n9. Merge all fusions detected by the selected tools with [Fusion-report](https://github.com/Clinical-Genomics/fusion-report)\n10. Post-processing and analysis of data\n - [FusionInspector](https://github.com/FusionInspector/FusionInspector)\n - Summarize information into a VCF file\n - [Arriba](https://github.com/suhrig/arriba) visualisation\n - Collect metrics ([`picard CollectRnaSeqMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037057492-CollectRnaSeqMetrics-Picard-)), [`picard CollectInsertSizeMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037055772-CollectInsertSizeMetrics-Picard-) and ([`GATK MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-))\n11. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n12. Compress bam files to cram with [samtools view](http://www.htslib.org/)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nAs the reference building is computationally heavy (> 24h on HPC), we had to use dummy reference files in the test profile. Therefore, it is recommended to run the test profile with the `-stub` option.\n\n```bash\nnextflow run nf-core/rnafusion \\\n -profile test, \\\n --outdir \\\n -stub\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n> **Notes:**\n>\n> - Conda is not currently supported; run with singularity or docker.\n> - Paths need to be absolute.\n> - GRCh38 is the only supported reference.\n> - Single-end reads are to be used as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp.\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnafusion/usage) and the [parameter documentation](https://nf-co.re/rnafusion/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnafusion/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnafusion/output).\n\n## Credits\n\nnf-core/rnafusion was written by Martin Proks ([@matq007](https://github.com/matq007)), Maxime Garcia ([@maxulysse](https://github.com/maxulysse)) and Annick Renevey ([@rannick](https://github.com/rannick))\n\n## We thank the following people for their help in the development of this pipeline\n\n- [Phil Ewels](https://github.com/ewels)\n- [Rickard Hammar\u00e9n](https://github.com/Hammarn)\n- [Alexander Peltzer](https://github.com/apeltzer)\n- [Praveen Raj](https://github.com/praveenraj2018)\n- [Anabella Trigila](https://github.com/atrigila)\n- [Nicolas Vannieuwkerke](https://github.com/nvnieuwk)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnafusion` channel](https://nfcore.slack.com/channels/rnafusion) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/rnafusion for your analysis, please cite it using the following doi: [10.5281/zenodo.3946477](https://doi.org/10.5281/zenodo.3946477)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" diff --git a/subworkflows/local/build_references/main.nf b/subworkflows/local/build_references/main.nf index 7ac3285a2..78d413709 100644 --- a/subworkflows/local/build_references/main.nf +++ b/subworkflows/local/build_references/main.nf @@ -24,7 +24,6 @@ include { SALMON_INDEX } from '../../../modules/nf-core/salmo include { FUSIONREPORT_DOWNLOAD } from '../../../modules/nf-core/fusionreport/download/main' include { STARFUSION_BUILD } from '../../../modules/nf-core/starfusion/build/main' include { GFFREAD } from '../../../modules/nf-core/gffread/main' -include { getFileSuffix } from '../../../modules/nf-core/cat/cat/main.nf' /* ======================================================================================== diff --git a/subworkflows/local/fusioninspector_workflow/main.nf b/subworkflows/local/fusioninspector_workflow/main.nf index 40257fa61..7324d8323 100644 --- a/subworkflows/local/fusioninspector_workflow/main.nf +++ b/subworkflows/local/fusioninspector_workflow/main.nf @@ -31,7 +31,7 @@ workflow FUSIONINSPECTOR_WORKFLOW { if (whitelist) { ch_whitelist = ch_fusion_list.combine(Channel.value(file(whitelist, checkIfExists:true))) - .map { meta, fusions, whitelist -> [ meta, [fusions, whitelist] ] } + .map { meta, fusions, whitelist_file -> [ meta, [fusions, whitelist_file] ] } CAT_CAT(ch_whitelist) // fusioninspector takes care of possible duplicates ch_versions = ch_versions.mix(CAT_CAT.out.versions) diff --git a/subworkflows/local/fusioninspector_workflow/tests/main.nf.test b/subworkflows/local/fusioninspector_workflow/tests/main.nf.test index e02352e94..746763ee7 100644 --- a/subworkflows/local/fusioninspector_workflow/tests/main.nf.test +++ b/subworkflows/local/fusioninspector_workflow/tests/main.nf.test @@ -110,7 +110,7 @@ nextflow_workflow { input[12] = false input[13] = true input[14] = 1 - input[15] = params.whitelist + input[15] = [] """ } } diff --git a/subworkflows/local/qc_workflow/main.nf b/subworkflows/local/qc_workflow/main.nf index a423471db..d83fea35c 100644 --- a/subworkflows/local/qc_workflow/main.nf +++ b/subworkflows/local/qc_workflow/main.nf @@ -19,9 +19,9 @@ workflow QC_WORKFLOW { PICARD_COLLECTRNASEQMETRICS( ch_bam_sorted, - ch_refflat.map{ _meta, refflat -> [ refflat ] }, - ch_fasta.map{ _meta, fasta -> [ fasta ] }, - ch_rrna_interval.map{ _meta, intervals -> [ intervals ] }.ifEmpty([]) + ch_refflat.map{ _meta, refflat -> refflat }, + ch_fasta.map{ _meta, fasta -> fasta }, + ch_rrna_interval.map{ _meta, intervals -> intervals } ) // Some chromosome or annotation may not have rRNA genes ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions) ch_rnaseq_metrics = PICARD_COLLECTRNASEQMETRICS.out.metrics diff --git a/subworkflows/local/qc_workflow/test/main.nf.test b/subworkflows/local/qc_workflow/test/main.nf.test index 2abb710e1..ba3053e95 100644 --- a/subworkflows/local/qc_workflow/test/main.nf.test +++ b/subworkflows/local/qc_workflow/test/main.nf.test @@ -13,8 +13,8 @@ nextflow_workflow { setup { // Create refflat reference - run("GTF_TO_REFFLAT") { - script "../../../../modules/local/uscs/custom_gtftogenepred/main.nf" + run("UCSC_GTFTOGENEPRED") { + script "../../../../modules/nf-core/ucsc/gtftogenepred/main.nf" process { """ input[0] =Channel.of( @@ -34,8 +34,8 @@ nextflow_workflow { """ input[0] = Channel.of( [ - [id: 'fasta'], - file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.gtf", checkIfExist: true) + [id: 'gtf'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.gtf", checkIfExists: true) ] ) """ @@ -60,8 +60,8 @@ nextflow_workflow { input[0] = AGAT_CONVERTGFF2BED.out.bed input[1] = Channel.of( [ - [id: 'chr22_dic'], - file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.dict", checkIfExist: true) + [id: 'chr22_dict'], + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) ] ) """ @@ -75,8 +75,9 @@ nextflow_workflow { params { skip_qc = false fusioninspector_only = false - starfusion = true - all = true + tools = "starfusion" + outdir = "test" + } workflow { @@ -89,12 +90,12 @@ nextflow_workflow { ]) // ch_refflat - input[1] = GTF_TO_REFFLAT.out.refflat.map { that -> [[id:that.Name], that] } + input[1] = UCSC_GTFTOGENEPRED.out.refflat // ch_fasta input[2] = Channel.of( [ [ id: "test_ref" ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExist: true) + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] ) @@ -102,12 +103,13 @@ nextflow_workflow { input[3] = Channel.of( [ [ id: "test_ref" ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExist: true) + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) ] ) // ch rRNA interval list input[4] = GATK4_BEDTOINTERVALLIST.out.interval_list """ + } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml deleted file mode 100644 index f84761125..000000000 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nextflow_pipeline: - - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml deleted file mode 100644 index ac8523c9a..000000000 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfcore_pipeline: - - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 09ef842ae..443e828cf 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -5,4 +5,4 @@ plugins { validation { parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" monochromeLogs = true -} \ No newline at end of file +} diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap index 7e0e54ae2..722144ae1 100644 --- a/tests/test_build.nf.test.snap +++ b/tests/test_build.nf.test.snap @@ -55,8 +55,6 @@ "agat/minigenome.gtf.bed", "bioawk", "bioawk/minigenome.gtf_rrna.gtf.gz", - "gatk4", - "gatk4/minigenome.dict", "pipeline_info", "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", @@ -68,6 +66,7 @@ "references/GRCh38/fusion_report_db/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", + "references/GRCh38/gencode_v46/gencode/minigenome.dict", "references/GRCh38/gencode_v46/gencode/minigenome.fa.fai", "references/GRCh38/gencode_v46/gencode/minigenome.gtf.fasta", "references/GRCh38/gencode_v46/gencode/minigenome.gtf.genepred", @@ -194,8 +193,8 @@ [ "minigenome.gtf.bed:md5,4c881266e0a1b1a41815d05a8055aa40", "minigenome.gtf_rrna.gtf.gz:md5,fb03ec66f68bc4becc71c299ed38b62d", - "minigenome.dict:md5,f2dfb8df1d1f860050fc0dba1399fd9e", "fusion_report.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "minigenome.dict:md5,f2dfb8df1d1f860050fc0dba1399fd9e", "minigenome.fa.fai:md5,e3f74a27219b33ae80fd5de5cbeaf32b", "minigenome.gtf.fasta:md5,349d42b5dbd73e163cdbad3453d8cd3a", "minigenome.gtf.genepred:md5,c5b0d2118efd89f7a2831e2dc486b999", @@ -287,6 +286,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:18:01.248835367" + "timestamp": "2025-09-05T12:58:07.878931" } } \ No newline at end of file diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap index 5a3a1bc32..e54f807af 100644 --- a/tests/test_stub.nf.test.snap +++ b/tests/test_stub.nf.test.snap @@ -82,8 +82,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -107,6 +105,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -237,7 +236,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:22:03.749618742" + "timestamp": "2025-09-04T17:13:34.296716" }, "stub test stringtie": { "content": [ @@ -320,8 +319,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -345,6 +342,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -402,7 +400,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:22:39.560551811" + "timestamp": "2025-09-04T17:15:18.001786" }, "stub test arriba": { "content": [ @@ -485,8 +483,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -510,6 +506,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -560,7 +557,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:19:38.026180355" + "timestamp": "2025-09-04T17:07:39.086364" }, "stub test fusioninspector": { "content": [ @@ -691,8 +688,6 @@ "fusionreport/test/test.fusions.csv", "fusionreport/test/test.fusions.json", "fusionreport/test/test_fusionreport_index.html", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -722,6 +717,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -853,7 +849,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:25:11.604461904" + "timestamp": "2025-09-04T17:21:42.479016" }, "stub test salmon": { "content": [ @@ -904,8 +900,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -921,6 +915,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/salmon", @@ -949,7 +944,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:24:28.067668122" + "timestamp": "2025-09-04T17:19:36.873298" }, "stub test ctatsplicing": { "content": [ @@ -1049,8 +1044,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1074,6 +1067,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -1205,7 +1199,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:20:13.319176919" + "timestamp": "2025-09-04T17:09:29.991365" }, "stub test fusionreport": { "content": [ @@ -1317,8 +1311,6 @@ "fusionreport/test/test.fusions.csv", "fusionreport/test/test.fusions.json", "fusionreport/test/test_fusionreport_index.html", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1348,6 +1340,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -1478,7 +1471,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:23:24.792491035" + "timestamp": "2025-09-04T17:17:14.759248" }, "stub test fastp": { "content": [ @@ -1535,8 +1528,6 @@ "fastqc_for_fastp", "fastqc_for_fastp/test_trimmed.html", "fastqc_for_fastp/test_trimmed.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1551,6 +1542,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai" ] @@ -1559,7 +1551,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:23:56.858216733" + "timestamp": "2025-09-04T17:18:27.651568" }, "stub test fusioncatcher": { "content": [ @@ -1608,8 +1600,6 @@ "fusioncatcher/test.fusion-genes.txt", "fusioncatcher/test.log", "fusioncatcher/test.summary.txt", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1624,6 +1614,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai" ] @@ -1632,7 +1623,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:20:49.030393254" + "timestamp": "2025-09-04T17:10:40.658609" }, "stub test fusioncatcher trim": { "content": [ @@ -1690,8 +1681,6 @@ "fusioncatcher/test.fusion-genes.txt", "fusioncatcher/test.log", "fusioncatcher/test.summary.txt", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1706,6 +1695,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai" ] @@ -1714,7 +1704,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:21:15.319414382" + "timestamp": "2025-09-04T17:11:47.659941" }, "stub test all": { "content": [ @@ -1903,8 +1893,6 @@ "fusionreport/test/test.fusions.csv", "fusionreport/test/test.fusions.json", "fusionreport/test/test_fusionreport_index.html", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1935,6 +1923,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/salmon", @@ -2102,6 +2091,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:19:03.489568486" + "timestamp": "2025-09-04T17:05:39.966652" } } \ No newline at end of file diff --git a/tests/test_stub_bam.nf.test.snap b/tests/test_stub_bam.nf.test.snap index af94c528c..5efbe384f 100644 --- a/tests/test_stub_bam.nf.test.snap +++ b/tests/test_stub_bam.nf.test.snap @@ -62,8 +62,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -87,6 +85,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -192,7 +191,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:29:13.77559568" + "timestamp": "2025-09-04T17:45:42.13657" }, "stub test stringtie": { "content": [ @@ -255,8 +254,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -280,6 +277,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -315,7 +313,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:29:53.58622226" + "timestamp": "2025-09-04T17:47:52.517978" }, "stub test arriba": { "content": [ @@ -378,8 +376,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -403,6 +399,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -428,7 +425,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:26:49.642086755" + "timestamp": "2025-09-04T17:40:41.686721" }, "stub test fusioninspector": { "content": [ @@ -539,8 +536,6 @@ "fusionreport/test/test.fusions.csv", "fusionreport/test/test.fusions.json", "fusionreport/test/test_fusionreport_index.html", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -570,6 +565,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -679,7 +675,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:32:46.154112416" + "timestamp": "2025-09-04T17:56:24.707034" }, "stub test salmon": { "content": [ @@ -740,8 +736,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -766,6 +760,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/salmon", @@ -794,7 +789,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:31:56.747683511" + "timestamp": "2025-09-04T17:54:08.811545" }, "stub test ctatsplicing": { "content": [ @@ -874,8 +869,6 @@ "fastqc", "fastqc/test.html", "fastqc/test.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -899,6 +892,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -1008,7 +1002,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:27:33.646044212" + "timestamp": "2025-09-04T17:42:17.062793" }, "stub test fusionreport": { "content": [ @@ -1100,8 +1094,6 @@ "fusionreport/test/test.fusions.csv", "fusionreport/test/test.fusions.json", "fusionreport/test/test_fusionreport_index.html", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1131,6 +1123,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/star", @@ -1236,7 +1229,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:30:34.704355039" + "timestamp": "2025-09-04T17:50:22.553497" }, "stub test fastp": { "content": [ @@ -1303,8 +1296,6 @@ "fastqc_for_fastp", "fastqc_for_fastp/test_trimmed.html", "fastqc_for_fastp/test_trimmed.zip", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1328,6 +1319,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai" ] @@ -1336,7 +1328,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:31:12.481382473" + "timestamp": "2025-09-04T17:52:24.935928" }, "stub test fusioncatcher": { "content": [ @@ -1395,8 +1387,6 @@ "fusioncatcher/test.fusion-genes.txt", "fusioncatcher/test.log", "fusioncatcher/test.summary.txt", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1420,6 +1410,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai" ] @@ -1428,7 +1419,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:28:10.779582543" + "timestamp": "2025-09-04T17:43:49.673677" }, "stub test all": { "content": [ @@ -1597,8 +1588,6 @@ "fusionreport/test/test.fusions.csv", "fusionreport/test/test.fusions.json", "fusionreport/test/test_fusionreport_index.html", - "gatk4", - "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", @@ -1629,6 +1618,7 @@ "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.genepred", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf.refflat", + "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46_dna_primary_assembly.fa.fai", "references/GRCh38/gencode_v46/salmon", @@ -1774,6 +1764,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-02T08:26:08.667543202" + "timestamp": "2025-09-04T17:39:00.417725" } } \ No newline at end of file