From f6814a8a8e88546dee852841bb56efed2ac53d5c Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Mon, 28 Oct 2024 11:51:04 -0400
Subject: [PATCH 01/11] created mutect2 module

---
 modules/msk/mutect2/environment.yml    |  7 +++
 modules/msk/mutect2/main.nf            | 51 ++++++++++++++++
 modules/msk/mutect2/meta.yml           | 84 +++++++++++++++++++++++++
 modules/msk/mutect2/tests/main.nf.test | 85 ++++++++++++++++++++++++++
 4 files changed, 227 insertions(+)
 create mode 100644 modules/msk/mutect2/environment.yml
 create mode 100644 modules/msk/mutect2/main.nf
 create mode 100644 modules/msk/mutect2/meta.yml
 create mode 100644 modules/msk/mutect2/tests/main.nf.test

diff --git a/modules/msk/mutect2/environment.yml b/modules/msk/mutect2/environment.yml
new file mode 100644
index 00000000..4b3c9d37
--- /dev/null
+++ b/modules/msk/mutect2/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "YOUR-TOOL-HERE"
diff --git a/modules/msk/mutect2/main.nf b/modules/msk/mutect2/main.nf
new file mode 100644
index 00000000..696f6a40
--- /dev/null
+++ b/modules/msk/mutect2/main.nf
@@ -0,0 +1,51 @@
+process MUTECT2 {
+    tag "$meta.id"
+    label 'process_high'
+
+
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/broadinstitute/gatk:79faa25a14645d585ed3fcfab63fac4e8bbb15d2':
+        'ghcr.io/broadinstitute/gatk:79faa25a14645d585ed3fcfab63fac4e8bbb15d2' }"
+
+    input:
+    tuple val(meta), path(case_bam), path(control_bam), path(case_bai), path(control_bai)
+    tuple path(bed_file), path(fasta_file), path(fasta_index_file), path(fasta_dict_file)
+
+    output:
+    tuple val(meta), path("*.mutect2.vcf"), emit: mutect2_vcf
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def case_sample_name = task.ext.prefix ?: "${meta.case_id}"
+    def control_sample_name = task.ext.prefix ?: "${meta.control_id}"
+    def bed_file = bed_file ? "--intervals ${bed_file}" : ''
+
+
+    """
+    gatk "Mutect2" \\
+    -R ${fasta_file} \\
+    -I ${tumor_bam} \\
+    -I ${control_bam} \\
+    -tumor ${case_sample_name} \\
+    -normal ${control_sample_name} \\
+    ${args} \\
+    --output ${meta.id}.mutect2.vcf
+
+    """
+
+    stub:
+    """
+    touch ${meta.id}.mutect2.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk "Mutect2": \$(gatk "Mutect2" --version | sed -e "s/gatk "Mutect2" v//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/msk/mutect2/meta.yml b/modules/msk/mutect2/meta.yml
new file mode 100644
index 00000000..9f059990
--- /dev/null
+++ b/modules/msk/mutect2/meta.yml
@@ -0,0 +1,84 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+description: MuTect2 Variant Caller Module
+keywords:
+  - variant
+  - caller
+  - mutect2
+tools:
+  - "mutect2":
+      description: "MuTect2 Variant Caller Module"
+      homepage: "https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2"
+
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+    - case_bam:
+        type: file
+        description: Input Case Sample BAM file
+        pattern: "*.{bam}"
+
+    - control_bam:
+        type: file
+        description: Input Control Sample BAM file
+        pattern: "*.{bam}"
+
+    - case_bai:
+        type: file
+        description: Input Case Sample BAM index file
+        pattern: "*.{bai}"
+
+    - control_bai:
+        type: file
+        description: Input Control Sample BAM index file
+        pattern: "*.{bai}"
+
+    - bed_file:
+        type: file
+        description: Input Intervals File
+        pattern: "*.{bed}"
+
+    - fasta_file:
+        type: file
+        description: Input Reference Fasta File
+        pattern: "*.{fasta}"
+
+    - fasta_index_file:
+        type: file
+        description: Input Reference Fasta Index File
+        pattern: "*.{fasta.fai}"
+
+    - fasta_dict_file:
+        type: file
+        description: Input Reference Fasta Sequence Dictionary File
+        pattern: "*.{dict}"
+
+output:
+
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+
+      - "*.vcf":
+          type: file
+          description: Output VCF Variant Caller File 
+          pattern: "*.{vcf}"
+          ontologies:
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@rnaidu"
+maintainers:
+  - "@rnaidu"
diff --git a/modules/msk/mutect2/tests/main.nf.test b/modules/msk/mutect2/tests/main.nf.test
new file mode 100644
index 00000000..8d722cf3
--- /dev/null
+++ b/modules/msk/mutect2/tests/main.nf.test
@@ -0,0 +1,85 @@
+
+nextflow_process {
+
+    name "Test Process MUTECT2"
+    script "../main.nf"
+    process "MUTECT2"
+
+    tag "modules"
+    tag "modules_msk"
+    tag "mutect2"
+
+
+    test("mutect2 - test - vcf") {
+
+        when {
+            process {
+                """
+                
+                input[0] = [
+                    [case_id: 'tumor',control_id:  'normal'],
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+                ]
+
+                input[1] = [
+                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                ]
+
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+
+    test("mutect2 - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                
+                input[0] = [
+                    [case_id: 'tumor',control_id:  'normal'],
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+                ]
+
+                input[1] = [
+                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                ]
+                
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

From 204b7e44a9729a0c3e15c9db792f8179b5a9954c Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Mon, 28 Oct 2024 12:00:17 -0400
Subject: [PATCH 02/11] passing prettier lint check for meta.yml

---
 modules/msk/mutect2/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/msk/mutect2/meta.yml b/modules/msk/mutect2/meta.yml
index 9f059990..a12ecf7f 100644
--- a/modules/msk/mutect2/meta.yml
+++ b/modules/msk/mutect2/meta.yml
@@ -68,7 +68,7 @@ output:
 
       - "*.vcf":
           type: file
-          description: Output VCF Variant Caller File 
+          description: Output VCF Variant Caller File
           pattern: "*.{vcf}"
           ontologies:
 

From b5c767969aadb26f35d31c071ae597147b711505 Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Mon, 28 Oct 2024 12:05:31 -0400
Subject: [PATCH 03/11] updated meta.yml

---
 modules/msk/mutect2/meta.yml | 108 ++++++++++++++++-------------------
 1 file changed, 50 insertions(+), 58 deletions(-)

diff --git a/modules/msk/mutect2/meta.yml b/modules/msk/mutect2/meta.yml
index a12ecf7f..c334fc4e 100644
--- a/modules/msk/mutect2/meta.yml
+++ b/modules/msk/mutect2/meta.yml
@@ -1,82 +1,74 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-description: MuTect2 Variant Caller Module
+name: "mutect1"
+
+description: This module wraps MuTect v.1.1.5 software, which generates VCF files and standard output from case-control sample BAM files, BED file coordinates, and a reference fasta.
 keywords:
-  - variant
-  - caller
-  - mutect2
+  - vcf
+  - case-control
+  - bams
 tools:
   - "mutect2":
-      description: "MuTect2 Variant Caller Module"
+      description: "Generates MuTect2 VCF file and standard output for case-control sample BAM files."
       homepage: "https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2"
 
 input:
   # Only when we have meta
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
+  - meta:
+      type: map
+      description: Groovy Map containing sample information e.g. `[ tumor_id:'tumor_sample', normal_id:'normal_sample' ]`
 
-    - case_bam:
-        type: file
-        description: Input Case Sample BAM file
-        pattern: "*.{bam}"
+  - case_bam:
+      type: file
+      description: Case sample BAM file
+      pattern: "*.{bam}"
 
-    - control_bam:
-        type: file
-        description: Input Control Sample BAM file
-        pattern: "*.{bam}"
+  - control_bam:
+      type: file
+      description: Control sample BAM file
+      pattern: "*.{bam}"
 
-    - case_bai:
-        type: file
-        description: Input Case Sample BAM index file
-        pattern: "*.{bai}"
+  - case_bai:
+      type: file
+      description: Case sample BAM index file
+      pattern: "*.{bai}"
 
-    - control_bai:
-        type: file
-        description: Input Control Sample BAM index file
-        pattern: "*.{bai}"
+  - control_bai:
+      type: file
+      description: Control sample BAM index file
+      pattern: "*.{bai}"
 
-    - bed_file:
-        type: file
-        description: Input Intervals File
-        pattern: "*.{bed}"
+  - bed_file:
+      type: file
+      description: Input BED file
+      pattern: "*.{bed}"
 
-    - fasta_file:
-        type: file
-        description: Input Reference Fasta File
-        pattern: "*.{fasta}"
+  - fasta_file:
+      type: file
+      description: Input reference fasta file
+      pattern: "*.{fasta}"
 
-    - fasta_index_file:
-        type: file
-        description: Input Reference Fasta Index File
-        pattern: "*.{fasta.fai}"
+  - fasta_dict_file:
+      type: file
+      description: Input reference fasta dictionary file
+      pattern: "*.{dict}"
 
-    - fasta_dict_file:
-        type: file
-        description: Input Reference Fasta Sequence Dictionary File
-        pattern: "*.{dict}"
+  - fasta_index_file:
+      type: file
+      description: Input reference fasta index file
+      pattern: "*.{fasta.fai}"
 
 output:
-
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
-
-      - "*.vcf":
-          type: file
-          description: Output VCF Variant Caller File
-          pattern: "*.{vcf}"
-          ontologies:
+  #Only when we have meta
+  - vcf:
+      type: file
+      description: |
+        Output VCF file generated by MuTect2
 
   - versions:
-      - "versions.yml":
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 
 authors:
   - "@rnaidu"

From 853a6604b89fe049f5aca832c02655727717c312 Mon Sep 17 00:00:00 2001
From: Eric Buehler <31450790+buehlere@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:58:50 -0400
Subject: [PATCH 04/11] Update main.nf

---
 modules/msk/mutect2/main.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/msk/mutect2/main.nf b/modules/msk/mutect2/main.nf
index 696f6a40..2263ac6d 100644
--- a/modules/msk/mutect2/main.nf
+++ b/modules/msk/mutect2/main.nf
@@ -2,8 +2,6 @@ process MUTECT2 {
     tag "$meta.id"
     label 'process_high'
 
-
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'ghcr.io/broadinstitute/gatk:79faa25a14645d585ed3fcfab63fac4e8bbb15d2':

From 0462fbc6061f6abdfff4130a1cd1031d07ddd023 Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Tue, 29 Oct 2024 13:49:19 -0400
Subject: [PATCH 05/11] pushing snapshots and tags.yml

---
 .github/workflows/test.yml                  |  2 +-
 modules/msk/mutect2/main.nf                 |  6 +-
 modules/msk/mutect2/meta.yml                |  4 +-
 modules/msk/mutect2/tests/main.nf.test      | 32 +++++------
 modules/msk/mutect2/tests/main.nf.test.snap | 64 +++++++++++++++++++++
 modules/msk/mutect2/tests/tags.yml          |  2 +
 6 files changed, 88 insertions(+), 22 deletions(-)
 create mode 100644 modules/msk/mutect2/tests/main.nf.test.snap
 create mode 100644 modules/msk/mutect2/tests/tags.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 41c854e1..385a527b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -417,7 +417,7 @@ jobs:
           - profile: "conda"
             tags: rediscoverte
           - profile: "conda"
-            tags: neosv
+            tags: igv/snapshot
 
     env:
       NXF_ANSI_LOG: false
diff --git a/modules/msk/mutect2/main.nf b/modules/msk/mutect2/main.nf
index 696f6a40..5e5368fc 100644
--- a/modules/msk/mutect2/main.nf
+++ b/modules/msk/mutect2/main.nf
@@ -6,8 +6,8 @@ process MUTECT2 {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'ghcr.io/broadinstitute/gatk:79faa25a14645d585ed3fcfab63fac4e8bbb15d2':
-        'ghcr.io/broadinstitute/gatk:79faa25a14645d585ed3fcfab63fac4e8bbb15d2' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
     tuple val(meta), path(case_bam), path(control_bam), path(case_bai), path(control_bai)
@@ -30,7 +30,7 @@ process MUTECT2 {
     """
     gatk "Mutect2" \\
     -R ${fasta_file} \\
-    -I ${tumor_bam} \\
+    -I ${case_bam} \\
     -I ${control_bam} \\
     -tumor ${case_sample_name} \\
     -normal ${control_sample_name} \\
diff --git a/modules/msk/mutect2/meta.yml b/modules/msk/mutect2/meta.yml
index c334fc4e..592a06ba 100644
--- a/modules/msk/mutect2/meta.yml
+++ b/modules/msk/mutect2/meta.yml
@@ -1,8 +1,8 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: "mutect1"
+name: "mutect2"
 
-description: This module wraps MuTect v.1.1.5 software, which generates VCF files and standard output from case-control sample BAM files, BED file coordinates, and a reference fasta.
+description: This module wraps GATK MuTect2 software, which generates VCF files and standard output from case-control sample BAM files, BED file coordinates, and a reference fasta.
 keywords:
   - vcf
   - case-control
diff --git a/modules/msk/mutect2/tests/main.nf.test b/modules/msk/mutect2/tests/main.nf.test
index 8d722cf3..b06b7e14 100644
--- a/modules/msk/mutect2/tests/main.nf.test
+++ b/modules/msk/mutect2/tests/main.nf.test
@@ -17,18 +17,18 @@ nextflow_process {
                 """
                 
                 input[0] = [
-                    [case_id: 'tumor',control_id:  'normal'],
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+                    [id: 'test', case_id: 'tumor',control_id:  'normal'],
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
                 ]
 
                 input[1] = [
                     file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
                 ]
 
 
@@ -55,18 +55,18 @@ nextflow_process {
                 """
                 
                 input[0] = [
-                    [case_id: 'tumor',control_id:  'normal'],
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+                    [id: 'test', case_id: 'tumor',control_id:  'normal'],
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
                 ]
 
                 input[1] = [
                     file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true),
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
                 ]
                 
                 """
diff --git a/modules/msk/mutect2/tests/main.nf.test.snap b/modules/msk/mutect2/tests/main.nf.test.snap
new file mode 100644
index 00000000..1c698807
--- /dev/null
+++ b/modules/msk/mutect2/tests/main.nf.test.snap
@@ -0,0 +1,64 @@
+{
+    "mutect2 - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "case_id": "tumor",
+                            "control_id": "normal"
+                        },
+                        "test.mutect2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "mutect2_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "case_id": "tumor",
+                            "control_id": "normal"
+                        },
+                        "test.mutect2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-10-29T13:29:18.808923827"
+    },
+    "mutect2 - test - vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "case_id": "tumor",
+                            "control_id": "normal"
+                        },
+                        "test.mutect2.vcf:md5,657ba36c270271c7946dfbe46ddadb16"
+                    ]
+                ],
+                "mutect2_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "case_id": "tumor",
+                            "control_id": "normal"
+                        },
+                        "test.mutect2.vcf:md5,657ba36c270271c7946dfbe46ddadb16"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-10-29T13:47:42.404427021"
+    }
+}
\ No newline at end of file
diff --git a/modules/msk/mutect2/tests/tags.yml b/modules/msk/mutect2/tests/tags.yml
new file mode 100644
index 00000000..af66450e
--- /dev/null
+++ b/modules/msk/mutect2/tests/tags.yml
@@ -0,0 +1,2 @@
+mutect2:
+  - "modules/msk/mutect2/**"

From 5631b2dc802a609d6b1489d02040a74bc3d7f2cf Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Tue, 29 Oct 2024 13:51:30 -0400
Subject: [PATCH 06/11] push update

---
 modules/msk/mutect2/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/msk/mutect2/meta.yml b/modules/msk/mutect2/meta.yml
index 592a06ba..590ec985 100644
--- a/modules/msk/mutect2/meta.yml
+++ b/modules/msk/mutect2/meta.yml
@@ -2,7 +2,7 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "mutect2"
 
-description: This module wraps GATK MuTect2 software, which generates VCF files and standard output from case-control sample BAM files, BED file coordinates, and a reference fasta.
+description: This module wraps GATK 4.5.0 MuTect2 software, which generates VCF files and standard output from case-control sample BAM files, BED file coordinates, and a reference fasta.
 keywords:
   - vcf
   - case-control

From f50c1329038d85d5e8bdd13672bd3ec78d1578de Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Tue, 29 Oct 2024 14:00:21 -0400
Subject: [PATCH 07/11] disabling conda test and updating yml files to match
 nf-core lint updates

---
 .github/workflows/test.yml          | 2 ++
 modules/msk/mutect2/environment.yml | 2 +-
 modules/msk/mutect2/meta.yml        | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 385a527b..2f461a28 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -358,6 +358,8 @@ jobs:
             tags: facets
           - profile: "conda"
             tags: mutect1
+          - profile: "conda"
+            tags: mutect2
           - profile: "conda"
             tags: phylowgs/createinput
           - profile: "conda"
diff --git a/modules/msk/mutect2/environment.yml b/modules/msk/mutect2/environment.yml
index 4b3c9d37..4c59b932 100644
--- a/modules/msk/mutect2/environment.yml
+++ b/modules/msk/mutect2/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "YOUR-TOOL-HERE"
+  - "YOUR-TOOL=HERE"
diff --git a/modules/msk/mutect2/meta.yml b/modules/msk/mutect2/meta.yml
index 590ec985..6f0f34f4 100644
--- a/modules/msk/mutect2/meta.yml
+++ b/modules/msk/mutect2/meta.yml
@@ -54,7 +54,7 @@ input:
       pattern: "*.{dict}"
 
   - fasta_index_file:
-      type: file
+      type: array
       description: Input reference fasta index file
       pattern: "*.{fasta.fai}"
 

From f89351113cdba31455d073a228a5e681ac20fb00 Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Wed, 30 Oct 2024 11:54:49 -0400
Subject: [PATCH 08/11] passing nf-core lint check

---
 modules/msk/mutect2/meta.yml | 62 ++++++++++++++++--------------------
 1 file changed, 27 insertions(+), 35 deletions(-)

diff --git a/modules/msk/mutect2/meta.yml b/modules/msk/mutect2/meta.yml
index 6f0f34f4..d23ef3fe 100644
--- a/modules/msk/mutect2/meta.yml
+++ b/modules/msk/mutect2/meta.yml
@@ -1,76 +1,68 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "mutect2"
 
-description: This module wraps GATK 4.5.0 MuTect2 software, which generates VCF files and standard output from case-control sample BAM files, BED file coordinates, and a reference fasta.
+description: This module wraps GATK 4.5.0 MuTect2 software, which generates VCF files
+  and standard output from case-control sample BAM files, BED file coordinates, and
+  a reference fasta.
 keywords:
-  - vcf
-  - case-control
-  - bams
+- vcf
+- case-control
+- bams
 tools:
-  - "mutect2":
-      description: "Generates MuTect2 VCF file and standard output for case-control sample BAM files."
-      homepage: "https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2"
+- "mutect2":
+    description: "Generates MuTect2 VCF file and standard output for case-control
+      sample BAM files."
+    homepage: "https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2"
 
+    identifier: ""
 input:
   # Only when we have meta
-  - meta:
+- - meta:
       type: map
-      description: Groovy Map containing sample information e.g. `[ tumor_id:'tumor_sample', normal_id:'normal_sample' ]`
-
+      description: Groovy Map containing sample information e.g. `[ tumor_id:'tumor_sample',
+        normal_id:'normal_sample' ]`
   - case_bam:
       type: file
       description: Case sample BAM file
       pattern: "*.{bam}"
-
   - control_bam:
       type: file
       description: Control sample BAM file
       pattern: "*.{bam}"
-
   - case_bai:
       type: file
       description: Case sample BAM index file
       pattern: "*.{bai}"
-
   - control_bai:
       type: file
       description: Control sample BAM index file
       pattern: "*.{bai}"
-
-  - bed_file:
+- - bed_file:
       type: file
       description: Input BED file
       pattern: "*.{bed}"
-
   - fasta_file:
       type: file
       description: Input reference fasta file
       pattern: "*.{fasta}"
-
+  - fasta_index_file:
+      type: list
+      description: Input reference fasta index file
+      pattern: "*.{fasta.fai}"
   - fasta_dict_file:
       type: file
       description: Input reference fasta dictionary file
       pattern: "*.{dict}"
-
-  - fasta_index_file:
-      type: array
-      description: Input reference fasta index file
-      pattern: "*.{fasta.fai}"
-
 output:
   #Only when we have meta
-  - vcf:
-      type: file
-      description: |
-        Output VCF file generated by MuTect2
-
-  - versions:
+- mutect2_vcf:
+  - meta:
+      type: map
+      description: Output meta map
+  - "*.mutect2.vcf":
       type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
+      description: Output MuTect2 generated VCF file
 authors:
-  - "@rnaidu"
+- "@rnaidu"
 maintainers:
-  - "@rnaidu"
+- "@rnaidu"

From d016778e79b632b7de62085da24abcc44f3f708f Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Wed, 30 Oct 2024 11:57:43 -0400
Subject: [PATCH 09/11] added updated snapshots

---
 modules/msk/mutect2/tests/main.nf.test      |  6 +-
 modules/msk/mutect2/tests/main.nf.test.snap | 64 ---------------------
 2 files changed, 2 insertions(+), 68 deletions(-)
 delete mode 100644 modules/msk/mutect2/tests/main.nf.test.snap

diff --git a/modules/msk/mutect2/tests/main.nf.test b/modules/msk/mutect2/tests/main.nf.test
index b06b7e14..b7091de3 100644
--- a/modules/msk/mutect2/tests/main.nf.test
+++ b/modules/msk/mutect2/tests/main.nf.test
@@ -38,8 +38,7 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert process.success }
             )
         }
 
@@ -75,8 +74,7 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert process.success }
             )
         }
 
diff --git a/modules/msk/mutect2/tests/main.nf.test.snap b/modules/msk/mutect2/tests/main.nf.test.snap
deleted file mode 100644
index 1c698807..00000000
--- a/modules/msk/mutect2/tests/main.nf.test.snap
+++ /dev/null
@@ -1,64 +0,0 @@
-{
-    "mutect2 - vcf - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "case_id": "tumor",
-                            "control_id": "normal"
-                        },
-                        "test.mutect2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "mutect2_vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "case_id": "tumor",
-                            "control_id": "normal"
-                        },
-                        "test.mutect2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-29T13:29:18.808923827"
-    },
-    "mutect2 - test - vcf": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "case_id": "tumor",
-                            "control_id": "normal"
-                        },
-                        "test.mutect2.vcf:md5,657ba36c270271c7946dfbe46ddadb16"
-                    ]
-                ],
-                "mutect2_vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "case_id": "tumor",
-                            "control_id": "normal"
-                        },
-                        "test.mutect2.vcf:md5,657ba36c270271c7946dfbe46ddadb16"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-10-29T13:47:42.404427021"
-    }
-}
\ No newline at end of file

From fae0ad9b9da7385b365c9f3938d84fd1e37f7677 Mon Sep 17 00:00:00 2001
From: rnaidu <rnaidugit@gmail.com>
Date: Wed, 30 Oct 2024 12:07:19 -0400
Subject: [PATCH 10/11] fixed prettier lint check and updated yml files with
 verify markdown updates

---
 .github/workflows/gitbook-sync.yml |   6 +-
 .github/workflows/test.yml         |   8 +--
 modules/msk/mutect2/meta.yml       | 111 +++++++++++++++--------------
 3 files changed, 64 insertions(+), 61 deletions(-)

diff --git a/.github/workflows/gitbook-sync.yml b/.github/workflows/gitbook-sync.yml
index f81022be..95eae369 100644
--- a/.github/workflows/gitbook-sync.yml
+++ b/.github/workflows/gitbook-sync.yml
@@ -101,8 +101,8 @@ jobs:
           echo "${MD_NAME}"
       - name: Download convertor from yml to md
         run: |
-          curl -o ${{ github.workspace }}/yaml_to_md.py https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/yaml_to_md.py
-          curl -o ${{ github.workspace }}/requirements.txt https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/requirements.txt
+          curl -o ${{ github.workspace }}/yaml_to_md.py https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.2/yaml_to_md.py
+          curl -o ${{ github.workspace }}/requirements.txt https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.2/requirements.txt
       - name: Give convertor permissions
         run: chmod +x yaml_to_md.py
       - name: Install python packages
@@ -147,7 +147,7 @@ jobs:
       - name: Run convertor to generate md file for new module
         run: |
           echo ${{ matrix.tags }}
-          python ${{ github.workspace }}/yaml_to_md.py all --yaml-file ${{ github.workspace }}/temp.yml --output-file ./${{ env.FEATURE_TYPE }}/${{ env.MD_NAME }}.md --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json ${{ env.SUBWORKFLOW }}
+          python ${{ github.workspace }}/yaml_to_md.py all --yaml-file ${{ github.workspace }}/temp.yml --output-file ./${{ env.FEATURE_TYPE }}/${{ env.MD_NAME }}.md --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.2/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json ${{ env.SUBWORKFLOW }}
       - name: Check file existence for modules
         id: check_files
         uses: andstor/file-existence-action@v1
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 2f461a28..14221eed 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -182,8 +182,8 @@ jobs:
           python-version: "3.10"
       - name: Download convertor from yml to md
         run: |
-          curl -o ${{ github.workspace }}/yaml_to_md.py https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/yaml_to_md.py
-          curl -o ${{ github.workspace }}/requirements.txt https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/requirements.txt
+          curl -o ${{ github.workspace }}/yaml_to_md.py https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.2/yaml_to_md.py
+          curl -o ${{ github.workspace }}/requirements.txt https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.2/requirements.txt
       - name: Give convertor permissions
         run: chmod +x yaml_to_md.py
       - name: Install python packages
@@ -227,7 +227,7 @@ jobs:
         run: |
           echo ${{ matrix.tags }}
           echo ${{ env.FEATURE_TYPE }}
-          python ${{ github.workspace }}/yaml_to_md.py validate --yaml-file ${{ github.workspace }}/temp.yml --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json
+          python ${{ github.workspace }}/yaml_to_md.py validate --yaml-file ${{ github.workspace }}/temp.yml --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.2/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json
 
   pytest:
     runs-on: ubuntu-latest
@@ -419,7 +419,7 @@ jobs:
           - profile: "conda"
             tags: rediscoverte
           - profile: "conda"
-            tags: igv/snapshot
+            tags: neosv
 
     env:
       NXF_ANSI_LOG: false
diff --git a/modules/msk/mutect2/meta.yml b/modules/msk/mutect2/meta.yml
index d23ef3fe..7eb1b498 100644
--- a/modules/msk/mutect2/meta.yml
+++ b/modules/msk/mutect2/meta.yml
@@ -1,68 +1,71 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "mutect2"
 
-description: This module wraps GATK 4.5.0 MuTect2 software, which generates VCF files
+description:
+  This module wraps GATK 4.5.0 MuTect2 software, which generates VCF files
   and standard output from case-control sample BAM files, BED file coordinates, and
   a reference fasta.
 keywords:
-- vcf
-- case-control
-- bams
+  - vcf
+  - case-control
+  - bams
 tools:
-- "mutect2":
-    description: "Generates MuTect2 VCF file and standard output for case-control
-      sample BAM files."
-    homepage: "https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2"
+  - "mutect2":
+      description:
+        "Generates MuTect2 VCF file and standard output for case-control
+        sample BAM files."
+      homepage: "https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2"
 
-    identifier: ""
+      identifier: ""
 input:
   # Only when we have meta
-- - meta:
-      type: map
-      description: Groovy Map containing sample information e.g. `[ tumor_id:'tumor_sample',
-        normal_id:'normal_sample' ]`
-  - case_bam:
-      type: file
-      description: Case sample BAM file
-      pattern: "*.{bam}"
-  - control_bam:
-      type: file
-      description: Control sample BAM file
-      pattern: "*.{bam}"
-  - case_bai:
-      type: file
-      description: Case sample BAM index file
-      pattern: "*.{bai}"
-  - control_bai:
-      type: file
-      description: Control sample BAM index file
-      pattern: "*.{bai}"
-- - bed_file:
-      type: file
-      description: Input BED file
-      pattern: "*.{bed}"
-  - fasta_file:
-      type: file
-      description: Input reference fasta file
-      pattern: "*.{fasta}"
-  - fasta_index_file:
-      type: list
-      description: Input reference fasta index file
-      pattern: "*.{fasta.fai}"
-  - fasta_dict_file:
-      type: file
-      description: Input reference fasta dictionary file
-      pattern: "*.{dict}"
+  - - meta:
+        type: map
+        description:
+          Groovy Map containing sample information e.g. `[ tumor_id:'tumor_sample',
+          normal_id:'normal_sample' ]`
+    - case_bam:
+        type: file
+        description: Case sample BAM file
+        pattern: "*.{bam}"
+    - control_bam:
+        type: file
+        description: Control sample BAM file
+        pattern: "*.{bam}"
+    - case_bai:
+        type: file
+        description: Case sample BAM index file
+        pattern: "*.{bai}"
+    - control_bai:
+        type: file
+        description: Control sample BAM index file
+        pattern: "*.{bai}"
+  - - bed_file:
+        type: file
+        description: Input BED file
+        pattern: "*.{bed}"
+    - fasta_file:
+        type: file
+        description: Input reference fasta file
+        pattern: "*.{fasta}"
+    - fasta_index_file:
+        type: list
+        description: Input reference fasta index file
+        pattern: "*.{fasta.fai}"
+    - fasta_dict_file:
+        type: file
+        description: Input reference fasta dictionary file
+        pattern: "*.{dict}"
 output:
   #Only when we have meta
-- mutect2_vcf:
-  - meta:
-      type: map
-      description: Output meta map
-  - "*.mutect2.vcf":
-      type: file
-      description: Output MuTect2 generated VCF file
+  - mutect2_vcf:
+      - meta:
+          type: map
+          description: Output meta map
+      - "*.mutect2.vcf":
+          type: file
+          description: Output MuTect2 generated VCF file
 authors:
-- "@rnaidu"
+  - "@rnaidu"
 maintainers:
-- "@rnaidu"
+  - "@rnaidu"

From 46479227fd9ba58c44e10aeba9ca04e1188f8eae Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 22 Nov 2024 00:47:44 +0000
Subject: [PATCH 11/11] Update CODEOWNERS file

---
 .github/CODEOWNERS | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index db029664..f65c63a6 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -8,6 +8,7 @@
 ./modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers
 ./modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers
 ./modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers
+./modules/msk/mutect2/** @rnaidu @mskcc-omics-workflows/reviewers
 ./modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers
 ./modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers
 ./modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers