- Completed mutect2_ms subwf for matched normal

- Separated test profile of mutect2_ms from other tools

conf/modules/mutect2.config

@@ -112,6 +112,7 @@ process {
         ]
     }
 
+// MULTI SAMPLE MUTECT2
     if (params.tools && params.tools.split(',').contains('mutect2_multi_sample')) {
         withName: 'MUTECT2_MS' {
             ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
@@ -126,6 +127,35 @@ process {
                 saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.id}/${it}" }
             ]
         }
+
+        withName: 'GETPILEUPSUMMARIES_MS.*' {
+            ext.prefix        = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
+            publishDir        = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/" },
+                pattern: "*.table",
+                saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.patient}/${it}" }
+            ]
+        }
+
+        withName: 'GATHERPILEUPSUMMARIES_MS.*' {
+            ext.prefix       = { "${meta.id}.mutect2" }
+            publishDir       = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/mutect2/${meta.patient}/" },
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: 'CALCULATECONTAMINATION_MS' {
+            ext.prefix       = { "${meta.id}.mutect2" }
+            ext.args         = { "-tumor-segmentation ${meta.id}.mutect2.segmentation.table" }
+            publishDir       = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/" },
+                saveAs: { filename -> filename.equals('versions.yml') ? null : "mutect2/${meta.patient}/${filename}" }
+            ]
+        }
     }
 
 

conf/test/test_tools_mutect2_ms.config

@@ -0,0 +1,23 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/sarek -profile test,<extra_test_profile>,<docker/singularity> --outdir <OUTDIR>
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    input                  = "${projectDir}/tests/csv/3.0/recalibrated_mutect2_ms.csv"
+    dbsnp                  = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
+    fasta                  = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
+    germline_resource      = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
+    intervals              = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
+    pon                    = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
+    nucleotides_per_second = 20
+    step                   = 'variant_calling'
+    tools                  = 'mutect2_multi_sample'
+    wes                    = true
+}

nextflow.config

@@ -226,6 +226,7 @@ profiles {
     split_fastq                { includeConfig 'conf/test/test_split_fastq.config' }
     targeted                   { includeConfig 'conf/test/test_targeted.config' }
     tools                      { includeConfig 'conf/test/test_tools.config' }
+    tools_mutect2_ms           { includeConfig 'conf/test/test_tools_mutect2_ms.config' }
     tools_germline             { includeConfig 'conf/test/test_tools_germline.config' }
     tools_somatic              { includeConfig 'conf/test/test_tools_somatic.config' }
     tools_somatic_ascat        { includeConfig 'conf/test/test_tools_somatic_ascat.config' }