From b4e81212549acb92743565aa080f5c3851f7e478 Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Tue, 1 Oct 2024 12:09:52 -0400
Subject: [PATCH] passing prettier and editorconfig checks

---
 modules/msk/genotypevariants/all/meta.yml | 148 +++++++++++-----------
 modules/msk/pvmaf/concat/meta.yml         |  70 +++++-----
 subworkflows/msk/traceback/main.nf        |   1 -
 3 files changed, 111 insertions(+), 108 deletions(-)

diff --git a/modules/msk/genotypevariants/all/meta.yml b/modules/msk/genotypevariants/all/meta.yml
index bc00b36b..72f0548a 100644
--- a/modules/msk/genotypevariants/all/meta.yml
+++ b/modules/msk/genotypevariants/all/meta.yml
@@ -2,83 +2,87 @@
 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"]
-    identifier: ''
+  - "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:
-      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
-- maf:
-  - 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:
-  - versions.yml:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+  - maf:
+      - 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:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
-- "@buehlere"
+  - "@buehlere"
 maintainers:
-- "@buehlere"
+  - "@buehlere"
diff --git a/modules/msk/pvmaf/concat/meta.yml b/modules/msk/pvmaf/concat/meta.yml
index 96595e3a..a34fdb6d 100644
--- a/modules/msk/pvmaf/concat/meta.yml
+++ b/modules/msk/pvmaf/concat/meta.yml
@@ -2,46 +2,46 @@
 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"]
-    identifier: ''
+  - "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:
-      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
-- 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"
+  - 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"
+  - "@buehlere"
 maintainers:
-- "@buehlere"
+  - "@buehlere"
diff --git a/subworkflows/msk/traceback/main.nf b/subworkflows/msk/traceback/main.nf
index 4f597ead..7123932a 100644
--- a/subworkflows/msk/traceback/main.nf
+++ b/subworkflows/msk/traceback/main.nf
@@ -27,7 +27,6 @@ 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]] }