updated meta and environment.ymls for traceback associated modulees t…

…o pass updated nf-core linting schema checks.

modules/msk/genotypevariants/all/meta.yml

@@ -1,20 +1,20 @@
----
 # 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:
-  - genotype
-  - bams
-  - maf
+- genotype
+- bams
+- maf
 tools:
-  - "genotypevariants":
-      description: "module supports genotyping and merging small variants (SNV and INDELS)."
-      documentation: "https://genotype-variants.readthedocs.io/en/latest/"
-      licence: ["MIT"]
+- "genotypevariants":
+    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:
+- - meta:
       type: map
       description: |
         Groovy Map containing sample information
@@ -25,54 +25,60 @@ input:
       pattern: "*.{bam}"
   - bai_standard:
       type: file
-      description: Requires the standard .bai file is present at same location as the bam 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.
+      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.
+      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:
+- - fasta:
       type: file
       description: The reference fasta file
       pattern: "*.fasta"
-  - fai:
+- - fai:
       type: file
       description: Index of reference fasta file
       pattern: "*.fasta.fai"
-
 output:
   #Only when we have meta
+- maf:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. `[ id:'sample1', patient:'patient_1' ]`
-  - maf:
+  - '*.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.
+      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:
+- versions:
+  - versions.yml:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
-  - "@buehlere"
+- "@buehlere"
 maintainers:
-  - "@buehlere"
+- "@buehlere"

modules/msk/pvmaf/concat/meta.yml

@@ -1,21 +1,21 @@
----
 # 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
 keywords:
-  - sort
-  - example
-  - genomics
+- sort
+- example
+- genomics
 tools:
-  - "pvmaf":
-      description: "provides a variety of commands for manipulating mafs."
-      homepage: "https://github.com/msk-access/postprocessing_variant_calls"
-      documentation: "https://cmo-ci.gitbook.io/postprocessing_variant_calls/"
-      licence: ["MIT"]
+- "pvmaf":
+    description: "provides a variety of commands for manipulating mafs."
+    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:
+- - meta:
       type: map
       description: |
         Groovy Map containing sample information
@@ -24,25 +24,24 @@ input:
       type: file
       description: list of maf files to concatenate
       pattern: "*.{maf}"
-
 output:
   #Only when we have meta
+- maf:
   - 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:
+  - '*.maf':
       type: file
       description: concatenated maf file
       pattern: "*.{maf}"
-
+- versions:
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
-  - "@buehlere"
+- "@buehlere"
 maintainers:
-  - "@buehlere"
+- "@buehlere"

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"

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
@@ -12,39 +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}"
-  - type:
-      type: string
-      description: The type of tagging to be performed.
-
+  - - 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 maf file.
-      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: