Update release candidate with fixes

.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

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"

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:

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"
     }
 }

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: