Add mitorsaw module for mitochondrial calling

assets/software_references.yml

@@ -195,3 +195,6 @@ tool:
   perl-math-cdf:
     citation: "perl-math-cdf"
     bibliography: ""
+  mitorsaw:
+    citation: "Mitorsaw"
+    bibliography: ""

conf/modules/call_mitochondrial_variants.config

@@ -0,0 +1,33 @@
+ /*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+
+process {
+
+    withName: '.*:CALL_MITOCHONDRIAL_VARIANTS:.*' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*:CALL_MITOCHONDRIAL_VARIANTS:DEEPVARIANT_RUNDEEPVARIANT' {
+        tag = {"${meta.id}_${meta.region.baseName}"}
+        ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" }
+        ext.args   = {
+            [
+                "--sample_name=${meta.id}",
+                "--model_type=${params.deepvariant_model_type}",
+                meta.sex == 1 ? '--haploid_contigs="chrX,chrY"' : '',
+            ].join(' ')
+        }
+    }
+}

conf/modules/gvcf_glnexus_norm_variants.config

@@ -19,9 +19,9 @@ process {
     }
 
     withName: '.*:GVCF_GLNEXUS_NORM_VARIANTS:VCFEXPRESS' {
-        ext.prefix = { "${meta.id}_${meta.sv_caller}_found_in" }
+        ext.prefix = { "${meta.id}_${meta.caller}_found_in" }
         ext.suffix = { "bcf.gz" }
-        ext.args = { "-s \'FOUND_IN=return \"${meta.sv_caller}\"\' -e \"return true\"" }
+        ext.args = { "-s \'FOUND_IN=return \"${meta.caller}\"\' -e \"return true\"" }
     }
 
     withName: '.*:GVCF_GLNEXUS_NORM_VARIANTS:GLNEXUS' {
@@ -51,4 +51,11 @@ process {
         ext.prefix = { intervals ? "${meta.id}_${intervals}_sentieon" : "${meta.id}_sentieon" }
     }
 
+    withName: '.*:GVCF_GLNEXUS_NORM_VARIANTS:BCFTOOLS_MERGE' {
+        ext.args = [
+            '--force-single'
+        ].join(' ')
+        ext.prefix = { "${meta.id}_merged" }
+    }
+
 }

main.nf

@@ -94,6 +94,7 @@ workflow GENOMICMEDICINESWEDEN_NALLO {
     val_phaser
     val_plot_chromograph_autozygosity
     val_plot_chromograph_coverage
+    val_preset
     val_pre_vep_snv_filter_expression
     val_run_methbat
     val_run_modkit
@@ -197,6 +198,7 @@ workflow GENOMICMEDICINESWEDEN_NALLO {
         val_phaser,
         val_plot_chromograph_autozygosity,
         val_plot_chromograph_coverage,
+        val_preset,
         val_pre_vep_snv_filter_expression,
         val_run_methbat,
         val_run_modkit,
@@ -324,6 +326,7 @@ workflow {
         params.phaser,
         params.plot_chromograph_autozygosity,
         params.plot_chromograph_coverage,
+        params.preset,
         params.pre_vep_snv_filter_expression,
         params.run_methbat,
         params.run_modkit,

modules.json

@@ -236,6 +236,11 @@
                         "git_sha": "14980f759266eec42dac401fcafeb83d6c957b41",
                         "installed_by": ["modules"]
                     },
+                    "mitorsaw/haplotype": {
+                        "branch": "master",
+                        "git_sha": "ae0ea82513abe5818d3c0b1026e78ca15c3bbf4f",
+                        "installed_by": ["modules"]
+                    },
                     "modkit/bedmethyltobigwig": {
                         "branch": "master",
                         "git_sha": "3d81317a30d1016b533982d6b84df07713ae520a",