diff --git a/modules/msk/genotypevariants/all/main.nf b/modules/msk/genotypevariants/all/main.nf index 40d3a081..05ab0665 100644 --- a/modules/msk/genotypevariants/all/main.nf +++ b/modules/msk/genotypevariants/all/main.nf @@ -39,7 +39,6 @@ process GENOTYPEVARIANTS_ALL { $bams_standard \\ $bam_liquid \\ $sample \\ - -t $task.cpus \\ $args cat <<-END_VERSIONS > versions.yml diff --git a/modules/msk/genotypevariants/all/meta.yml b/modules/msk/genotypevariants/all/meta.yml index a5e7d9e0..a8f3c373 100644 --- a/modules/msk/genotypevariants/all/meta.yml +++ b/modules/msk/genotypevariants/all/meta.yml @@ -1,5 +1,4 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +## yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "genotypevariants_all" description: write your description here keywords: @@ -11,67 +10,78 @@ tools: description: "module supports genotyping and merging small variants (SNV and INDELS)." documentation: "https://genotype-variants.readthedocs.io/en/latest/" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', patient:'patient_1' ]` - - bam_standard: - type: file - description: Full path to standard bam file. - pattern: "*.{bam}" - - bai_standard: - type: file - description: Requires the standard .bai file is present at same location as the bam file. - pattern: "*.{bai}" - - bam_duplex: - type: file - description: Full path to duplex bam file. - pattern: "*.{bam}" - - bai_duplex: - type: file - description: Requires the duplex .bai file is present at same location as the bam file. - pattern: "*.{bai}" - - bam_simplex: - type: file - description: Full path to simplex bam file. - pattern: "*.{bam}" - - bai_simplex: - type: file - description: Requires the simplex .bai file is present at same location as the bam file. - pattern: "*.{bai}" - - maf: - type: file - description: Full path to small variants input file in MAF format - pattern: "*.{maf}" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', patient:'patient_1' ]` + - bam_standard: + type: file + description: Full path to standard bam file. + pattern: "*.{bam}" + - bai_standard: + type: file + description: + Requires the standard .bai file is present at same location as + the bam file. + pattern: "*.{bai}" + - bam_duplex: + type: file + description: Full path to duplex bam file. + pattern: "*.{bam}" + - bai_duplex: + type: file + description: + Requires the duplex .bai file is present at same location as the + bam file. + pattern: "*.{bai}" + - bam_simplex: + type: file + description: Full path to simplex bam file. + pattern: "*.{bam}" + - bai_simplex: + type: file + description: + Requires the simplex .bai file is present at same location as the + bam file. + pattern: "*.{bai}" + - maf: + type: file + description: Full path to small variants input file in MAF format + pattern: "*.{maf}" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', patient:'patient_1' ]` - maf: - type: file - description: Genotyped maf for each bam provided and a merged genotyped maf. The mafs will be labelled with patient identifier or sample identifier as the prefix, and end with the type of bam (duplex, simplex, or standard). The sample identifier is prioritized. - pattern: "*.{mafs}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', patient:'patient_1' ]` + - "*.maf": + type: file + description: + Genotyped maf for each bam provided and a merged genotyped maf. + The mafs will be labelled with patient identifier or sample identifier as + the prefix, and end with the type of bam (duplex, simplex, or standard). The + sample identifier is prioritized. + pattern: "*.{mafs}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@buehlere" maintainers: diff --git a/modules/msk/pvmaf/concat/main.nf b/modules/msk/pvmaf/concat/main.nf index bb12148f..225751be 100644 --- a/modules/msk/pvmaf/concat/main.nf +++ b/modules/msk/pvmaf/concat/main.nf @@ -4,8 +4,8 @@ process PVMAF_CONCAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'ghcr.io/msk-access/postprocessing_variant_calls:0.3.0': - 'ghcr.io/msk-access/postprocessing_variant_calls:0.3.0' }" + 'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6': + 'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }" input: tuple val(meta), path(maf_files, stageAs: "*?-ORG-SIMPLEX-DUPLEX_genotyped.maf")// [ id:'sample1', patient:'patient1' ], [maf_1, ... maf_n] diff --git a/modules/msk/pvmaf/concat/meta.yml b/modules/msk/pvmaf/concat/meta.yml index f676983e..a34fdb6d 100644 --- a/modules/msk/pvmaf/concat/meta.yml +++ b/modules/msk/pvmaf/concat/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "pvmaf_concat" description: a flexible command for concatenating maf files @@ -12,36 +11,36 @@ tools: homepage: "https://github.com/msk-access/postprocessing_variant_calls" documentation: "https://cmo-ci.gitbook.io/postprocessing_variant_calls/" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', patient:'patient1' ]` - - maf_files: - type: file - description: list of maf files to concatenate - pattern: "*.{maf}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', patient:'patient1' ]` + - maf_files: + type: file + description: list of maf files to concatenate + pattern: "*.{maf}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', patient:'patient1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: concatenated maf file - pattern: "*.{maf}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', patient:'patient1' ]` + - "*.maf": + type: file + description: concatenated maf file + pattern: "*.{maf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@buehlere" maintainers: diff --git a/modules/msk/pvmaf/concat/tests/main.nf.test.snap b/modules/msk/pvmaf/concat/tests/main.nf.test.snap index a6626e47..71ed98cc 100644 --- a/modules/msk/pvmaf/concat/tests/main.nf.test.snap +++ b/modules/msk/pvmaf/concat/tests/main.nf.test.snap @@ -28,7 +28,11 @@ ] } ], - "timestamp": "2024-02-23T11:31:39.015292" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.2" + }, + "timestamp": "2024-10-01T12:18:30.061693329" }, "chr22maf - msk": { "content": [ @@ -39,7 +43,7 @@ "id": "chr22", "patient": "test" }, - "test_combined.maf:md5,7b36c0fda7ebb28b27ddf51b7d2a09e8" + "test_combined.maf:md5,e1d7d2ecaf53ce75908ad49b25289f32" ] ], "1": [ @@ -51,7 +55,7 @@ "id": "chr22", "patient": "test" }, - "test_combined.maf:md5,7b36c0fda7ebb28b27ddf51b7d2a09e8" + "test_combined.maf:md5,e1d7d2ecaf53ce75908ad49b25289f32" ] ], "versions": [ @@ -59,6 +63,10 @@ ] } ], - "timestamp": "2024-02-23T11:31:28.145005" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.2" + }, + "timestamp": "2024-10-01T12:18:20.94747798" } } \ No newline at end of file diff --git a/modules/msk/pvmaf/tagtraceback/environment.yml b/modules/msk/pvmaf/tagtraceback/environment.yml index b461aeda..4c59b932 100644 --- a/modules/msk/pvmaf/tagtraceback/environment.yml +++ b/modules/msk/pvmaf/tagtraceback/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "pvmaf_tagtraceback" channels: - conda-forge - bioconda - - defaults dependencies: - - "YOUR-TOOL-HERE" + - "YOUR-TOOL=HERE" diff --git a/modules/msk/pvmaf/tagtraceback/main.nf b/modules/msk/pvmaf/tagtraceback/main.nf index 27f4c164..bee0144e 100644 --- a/modules/msk/pvmaf/tagtraceback/main.nf +++ b/modules/msk/pvmaf/tagtraceback/main.nf @@ -1,14 +1,15 @@ process PVMAF_TAGTRACEBACK { tag "$meta.id" label 'process_single' + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'ghcr.io/msk-access/postprocessing_variant_calls:type_traceback_0.0.7': - 'ghcr.io/msk-access/postprocessing_variant_calls:type_traceback_0.0.7' }" + 'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6': + 'ghcr.io/msk-access/postprocessing_variant_calls:0.2.6' }" input: - tuple val(meta), path(maf) // [ id:'sample1', patient:'patient1' ], *.maf - path(sample_sheets) // [samplesheet_1, ..., samplesheet_n] + tuple val(meta), path(maf) + path(sample_sheets) output: tuple val(meta), path("*.maf"), emit: maf diff --git a/modules/msk/pvmaf/tagtraceback/meta.yml b/modules/msk/pvmaf/tagtraceback/meta.yml index 7e5fa336..a6c74526 100644 --- a/modules/msk/pvmaf/tagtraceback/meta.yml +++ b/modules/msk/pvmaf/tagtraceback/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "pvmaf_tagtraceback" description: a flexible command for tagging maf files @@ -12,43 +11,39 @@ tools: homepage: "https://github.com/msk-access/postprocessing_variant_calls" documentation: "https://cmo-ci.gitbook.io/postprocessing_variant_calls/" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', patient:'patient1' ]` - - - maf: - type: file - description: Maf file with columns required for selected tagging type. - pattern: "*.{maf}" - - - path(sample_sheets): - type: file - description: | - Samplesheet with `sample_id` and `type` columns. - Used to add fillout type information to provided maf. - See Nucleovar for more info: https://github.com/mskcc-omics-workflows/nucleovar/blob/main/README.md. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', patient:'patient1' ]` + - maf: + type: file + description: Maf file with columns required for selected tagging type. + pattern: "*.{maf}" + - - sample_sheets: + type: list + description: array holding the two samplesheets mandatory for running nucleovar, (pipeline_input and aux_bams) output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', patient:'patient1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: tagged traceback maf. - pattern: "*.{maf}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', patient:'patient1' ]` + - "*.maf": + type: file + description: tagged maf file. + pattern: "*.{maf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@buehlere" maintainers: diff --git a/subworkflows/msk/traceback/main.nf b/subworkflows/msk/traceback/main.nf index f51b5c6f..7123932a 100644 --- a/subworkflows/msk/traceback/main.nf +++ b/subworkflows/msk/traceback/main.nf @@ -27,12 +27,12 @@ workflow TRACEBACK { .map {it -> [it[0].subMap('patient')[0], *it[1..-1]] } .set{concat_maf} + bams .map { it -> [it[0].subMap('patient')[0], it[0], *it[1..-1]] } .combine(concat_maf, by:0) .map { it[1..-1] } .set{bam_list_maf} - // genotype each bam combined maf, per patient if provided GENOTYPEVARIANTS_ALL(bam_list_maf, reference, reference_fai) ch_versions = ch_versions.mix(GENOTYPEVARIANTS_ALL.out.versions.first())