vardictjava variant calling workflow

conf/modules/vardictjava.config

@@ -0,0 +1,36 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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.
+        ext.when   = When to run the module.
+----------------------------------------------------------------------------------------
+*/
+
+process{
+        withName: 'VARDICTJAVA' {
+        ext.args   = { "-c 1 -S 2 -E 3 -g 4 --nosv --deldupvar -Q 10 -F 0x700 -f 0.1 -N ${meta.sample}_${meta.patient}"} //
+        ext.args2  = { "-f 0.1 -A -N ${meta.sample}_${meta.patient}" }
+        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.vardictjava" : "${meta.id}.vardictjava.${intervals.simpleName}" }
+        ext.when   = { params.tools && params.tools.split(',').contains('vardictjava') }
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/" },
+            pattern: "*{vcf.gz,vcf.gz.tbi}",
+            saveAs: { meta.num_intervals > 1 ? null : "vardictjava/${meta.id}/${it}" }
+        ]
+    }
+
+    withName: 'MERGE_VARDICTJAVA' {
+        ext.prefix = { "${meta.id}.vardictjava" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/vardictjava/${meta.id}/" },
+            pattern: "*{vcf.gz,vcf.gz.tbi}"
+        ]
+    }
+}

modules.json

@@ -494,6 +494,11 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
+                    "vardictjava": {
+                        "branch": "master",
+                        "git_sha": "27e170816808aedbbac23f9a1f2c7488d4b6d342",
+                        "installed_by": ["modules"]
+                    },
                     "vcftools": {
                         "branch": "master",
                         "git_sha": "624ecdc43b72e0a45bf05d9b57215d18dcd538f8",

nextflow.config

@@ -442,6 +442,7 @@ includeConfig 'conf/modules/sentieon_haplotyper_joint_germline.config'
 includeConfig 'conf/modules/strelka.config'
 includeConfig 'conf/modules/tiddit.config'
 includeConfig 'conf/modules/post_variant_calling.config'
+includeConfig 'conf/modules/vardictjava.config'
 
 //annotate
 includeConfig 'conf/modules/annotate.config'

nextflow_schema.json

@@ -111,8 +111,8 @@
                     "type": "string",
                     "fa_icon": "fas fa-toolbox",
                     "description": "Tools to use for duplicate marking, variant calling and/or for annotation.",
-                    "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Strelka\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively), and bcftools annotate (needs `--bcftools_annotation`).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.",
-                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
+                    "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Strelka\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively), VarDictJava and bcftools annotate (needs `--bcftools_annotation`).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.",
+                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vardictjava|vep)?,?)*(?<!,)$"
                 },
                 "skip_tools": {
                     "type": "string",