Add deepsomatic tool

conf/modules/deepsomatic.config

@@ -0,0 +1,43 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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.
+----------------------------------------------------------------------------------------
+*/
+
+// DEEPVARIANT
+
+process {
+
+    withName: 'DEEPSOMATIC' {
+        ext.args   = { params.wes ?  "--model_type WES" : "--model_type WGS" }
+        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepsomatic" : "${meta.id}.deepsomatic.${intervals.baseName}" }
+        ext.when   = { params.tools && params.tools.split(',').contains('deepsomatic') }
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/" },
+            pattern: "*{vcf.gz,vcf.gz.tbi}",
+            saveAs: { meta.num_intervals > 1 ? null : "deepsomatic/${meta.id}/${it}" }
+        ]
+    }
+
+    withName: 'MERGE_DEEPSOMATIC_.*' {
+        ext.prefix = { "${meta.id}.deepsomatic" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/deepsomatic/${meta.id}/" },
+            pattern: "*{vcf.gz,vcf.gz.tbi}"
+        ]
+    }
+
+    withName: 'MERGE_DEEPSOMATIC_GVCF' {
+        ext.prefix = { "${meta.id}.deepsomatic.g" }
+    }
+
+}

modules.json

@@ -122,7 +122,12 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "deepvariant/rundeepvariant": {
+                    "deepsomatic": {
+                        "branch": "master",
+                        "git_sha": "89e06f63c5ee7abe5d6910277aff8e83b00a8b50",
+                        "installed_by": ["modules"]
+                    },
+                    "deepvariant": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]

nextflow.config

@@ -458,6 +458,7 @@ includeConfig 'conf/modules/ascat.config'
 includeConfig 'conf/modules/cnvkit.config'
 includeConfig 'conf/modules/controlfreec.config'
 includeConfig 'conf/modules/deepvariant.config'
+includeConfig 'conf/modules/deepsomatic.config'
 includeConfig 'conf/modules/freebayes.config'
 includeConfig 'conf/modules/haplotypecaller.config'
 includeConfig 'conf/modules/indexcov.config'

nextflow_schema.json

@@ -112,7 +112,7 @@
                     "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: indexcov, 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, Lofreq, 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, Strelka2\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|lofreq|sentieon_dnascope|sentieon_haplotyper|manta|indexcov|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
+                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|deepsomatic|freebayes|haplotypecaller|lofreq|sentieon_dnascope|sentieon_haplotyper|manta|indexcov|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
                 },
                 "skip_tools": {
                     "type": "string",