From b70d754cb2ad530530dd3197527bf736d9760ef2 Mon Sep 17 00:00:00 2001 From: Nikhil Kumar Date: Thu, 5 Feb 2026 12:02:37 -0500 Subject: [PATCH 1/2] Fix tests --- modules/msk/generatemutfasta/1.2/meta.yml | 5 +- modules/msk/mutalyzer/retriever/meta.yml | 2 +- .../mafannotate/tests/main.nf.test.snap | 8 +- .../msk/generate_mutated_peptides/meta.yml | 83 +++++++------------ 4 files changed, 36 insertions(+), 62 deletions(-) diff --git a/modules/msk/generatemutfasta/1.2/meta.yml b/modules/msk/generatemutfasta/1.2/meta.yml index 885f44a8..4691c675 100644 --- a/modules/msk/generatemutfasta/1.2/meta.yml +++ b/modules/msk/generatemutfasta/1.2/meta.yml @@ -18,7 +18,7 @@ tools: description: "A tool primarily designed to check descriptions of sequence variants according to the Human Genome Sequence Variation Society (HGVS) guidelines." documentation: "https://mutalyzer.readthedocs.io/en/latest/" licence: ["MIT"] - identifier: "mutalyzer" + identifier: "" input: - - meta: @@ -30,8 +30,7 @@ input: type: file description: Maf outputtted by Tempo that was run through phyloWGS pattern: "*.maf" - - mutalyzer_cache: - - "*.tar.gz": + - - mutalyzer_cache: type: file description: Mutatalyzer cache to use with the normalizer pattern: "*.tar.gz" diff --git a/modules/msk/mutalyzer/retriever/meta.yml b/modules/msk/mutalyzer/retriever/meta.yml index 83fd2d22..268ae4e8 100644 --- a/modules/msk/mutalyzer/retriever/meta.yml +++ b/modules/msk/mutalyzer/retriever/meta.yml @@ -13,7 +13,7 @@ tools: description: "A tool primarily designed to check descriptions of sequence variants according to the Human Genome Sequence Variation Society (HGVS) guidelines." documentation: "https://mutalyzer.readthedocs.io/en/latest/" licence: ["MIT"] - identifier: "mutalyzer" + identifier: "" input: - - meta: diff --git a/modules/msk/oncokb/mafannotate/tests/main.nf.test.snap b/modules/msk/oncokb/mafannotate/tests/main.nf.test.snap index 4c05b143..bbbbf73e 100644 --- a/modules/msk/oncokb/mafannotate/tests/main.nf.test.snap +++ b/modules/msk/oncokb/mafannotate/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "case_id": "sample1", "control_id": "sample2" }, - "test.oncokb.maf:md5,dd58c4431ec26cb47fb97236d063c6a5" + "test.oncokb.maf:md5,4e544b3224d3a237b78c8d9a446d5541" ] ], "1": [ @@ -22,7 +22,7 @@ "case_id": "sample1", "control_id": "sample2" }, - "test.oncokb.maf:md5,dd58c4431ec26cb47fb97236d063c6a5" + "test.oncokb.maf:md5,4e544b3224d3a237b78c8d9a446d5541" ] ], "versions": [ @@ -32,8 +32,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.04.4" + "nextflow": "25.10.2" }, - "timestamp": "2025-03-03T13:18:05.707580942" + "timestamp": "2026-02-05T11:09:58.592758567" } } \ No newline at end of file diff --git a/subworkflows/msk/generate_mutated_peptides/meta.yml b/subworkflows/msk/generate_mutated_peptides/meta.yml index 5e358643..f15ae7fc 100644 --- a/subworkflows/msk/generate_mutated_peptides/meta.yml +++ b/subworkflows/msk/generate_mutated_peptides/meta.yml @@ -1,6 +1,6 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json name: "generate_mutated_peptides" -description: Generate mutated peptides from an annpotated MAF +description: Generate mutated peptides from an annotated MAF keywords: - peptides - maf @@ -12,26 +12,15 @@ components: - neoantigenutils/generatemutfasta input: - ch_maf_hla_sv: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf - type: file - description: | - The input containing the maf file - pattern: "*.{maf}" - - hla - type: file - description: | - The input containing the hla file - pattern: "*.{hla.txt}" - - sv - type: file - description: | - The input containing the sv file - pattern: "*.{bedpe}" + type: object + description: | + Object containing sample metadata and input files. + Properties: + - meta: Groovy Map containing sample information, e.g. [ id:'sample1', single_end:false ] + - maf: The input containing the maf file + - hla: The input containing the hla file + - sv: The input containing the sv file + pattern: "*.{maf,hla.txt,bedpe}" - ref_fasta: type: file description: A gzipped Human fasta file, ideally compressed with bgzip @@ -46,45 +35,31 @@ input: pattern: "*.{gtf.gz}" - cdna: type: file - description: | - The resource channel containing the cdna file + description: The resource channel containing the cdna file pattern: "*.{fa.gz}" output: - mut_fasta: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - "*_out/*.MUT.sequences.fa": - type: file - description: Mutated fasta sequence - pattern: "*.MUT.sequences.fa" + type: file + description: | + Mutated fasta sequence output. + Contains: meta (Groovy Map with sample information) and mutated sequences file + pattern: "*_out/*.MUT.sequences.fa" - wt_fasta: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - "*_out/*.WT.sequences.fa": - type: file - description: Wildtype fasta sequence - pattern: "*.WT.sequences.fa" + type: file + description: | + Wildtype fasta sequence output. + Contains: meta (Groovy Map with sample information) and wildtype sequences file + pattern: "*_out/*.WT.sequences.fa" - mut_fasta_log: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - "*_out/*_generate_mut_fasta.log": - type: file - description: Log file for the mutated fasta generation - pattern: "*_generate_mut_fasta.log" + type: file + description: | + Log file for the mutated fasta generation. + Contains: meta (Groovy Map with sample information) and generation log + pattern: "*_out/*_generate_mut_fasta.log" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nikhil" maintainers: From 4daebc5e3485e724b3a0557056edb52074666bdb Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 5 Feb 2026 19:53:58 +0000 Subject: [PATCH 2/2] update CODEOWNERS file --- .github/CODEOWNERS | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 48a786e4..ca8993c2 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -37,7 +37,7 @@ modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers -subworkflows/msk/generate_mutated_peptides/** @mskcc-omics-workflows/reviewers +subworkflows/msk/generate_mutated_peptides/** @nikhil @mskcc-omics-workflows/reviewers subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers