Using GATKs mergeVcfs

CHANGELOG.md

@@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [#571](https://github.com/nf-core/sarek/pull/571) - Including and using GATK4's mergeVcfs. Removing the local module `concat_vcf`.
 - [#383](https://github.com/nf-core/sarek/pull/383), [#528](https://github.com/nf-core/sarek/pull/528) - Update `CHANGELOG`
 - [#390](https://github.com/nf-core/sarek/pull/390) - Update `nextflow_schema.json`
 - [#408](https://github.com/nf-core/sarek/pull/408) - Sync `TEMPLATE` with `tools` `2.0.1`

README.md

@@ -91,6 +91,7 @@ We thank the following people for their extensive assistance in the development
 - [Abhinav Sharma](https://github.com/abhi18av)
 - [Adrian Lärkeryd](https://github.com/adrlar)
 - [Alexander Peltzer](https://github.com/apeltzer)
+- [Anders Sune Pedersen](https://github.com/asp8200)
 - [Chela James](https://github.com/chelauk)
 - [David Mas-Ponte](https://github.com/davidmasp)
 - [Francesco L](https://github.com/nibscles)

conf/modules.config

@@ -470,28 +470,15 @@ process {
 
 // VARIANT CALLING
 process{
-    // ALL
-    withName: 'CONCAT_.*' {
-        // For unknown reasons, CONCAT_VCF sometimes fails with SIGPIPE
-        // (exit code 141). Rerunning the process will usually work.
-        errorStrategy   = {task.exitStatus == 141 ? 'retry' : 'terminate'}
-        ext.args         = { params.no_intervals ?  "-n" : "" } //Why ConcatVCF is never run when no_intervals is set..
-    }
-    withName : 'BGZIP_VC_.*' {
-        publishDir       = [
-            enabled: false
-        ]
-    }
-
     // DEEPVARIANT
-    withName: 'CONCAT_DEEPVARIANT_.*' {
+    withName: 'MERGE_DEEPVARIANT_.*' {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" },
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
-    withName: 'CONCAT_DEEPVARIANT_GVCF' {
+    withName: 'MERGE_DEEPVARIANT_GVCF' {
         ext.prefix       = {"${meta.id}.g"}
     }
     withName: 'DEEPVARIANT' {
@@ -513,7 +500,7 @@ process{
     }
 
     // FREEBAYES
-    withName: 'CONCAT_FREEBAYES' {
+    withName: 'MERGE_FREEBAYES' {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
@@ -547,7 +534,7 @@ process{
     }
 
     // HAPLOTYPECALLER
-    withName: 'CONCAT_HAPLOTYPECALLER' {
+    withName: 'MERGE_HAPLOTYPECALLER' {
         ext.prefix       = {"${meta.id}.g"}
         publishDir       = [
             enabled: !params.no_intervals,
@@ -578,20 +565,20 @@ process{
     }
 
     // MANTA
-    withName: 'CONCAT_MANTA.*' {
+    withName: 'MERGE_MANTA.*' {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/manta" },
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
-    withName: 'CONCAT_MANTA_DIPLOID' {
+    withName: 'MERGE_MANTA_DIPLOID' {
         ext.prefix       = {"${meta.id}.diploid_sv"}
     }
-    withName: 'CONCAT_MANTA_SMALL_INDELS' {
+    withName: 'MERGE_MANTA_SMALL_INDELS' {
         ext.prefix       = {"${meta.id}.candidate_small_indels"}
     }
-    withName: 'CONCAT_MANTA_SV' {
+    withName: 'MERGE_MANTA_SV' {
         ext.prefix       = {"${meta.id}.candidate_sv"}
     }
     withName: 'MANTA.*' {
@@ -606,17 +593,17 @@ process{
     }
 
     // STRELKA
-    withName: 'CONCAT_STRELKA.*' {
+    withName: 'MERGE_STRELKA.*' {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/strelka" },
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
-    withName: 'CONCAT_STRELKA' {
+    withName: 'MERGE_STRELKA' {
         ext.prefix       = {"${meta.id}.variants"}
     }
-    withName: 'CONCAT_STRELKA_GENOME' {
+    withName: 'MERGE_STRELKA_GENOME' {
         ext.prefix       = {"${meta.id}.genome"}
     }
     withName: 'STRELKA_.*' {
@@ -736,7 +723,7 @@ process{
     }
 
     //MANTA
-    withName: 'CONCAT_MANTA_TUMOR' {
+    withName: 'MERGE_MANTA_TUMOR' {
         ext.prefix       = {"${meta.id}.tumor_sv"}
     }
 
@@ -750,7 +737,7 @@ process{
         ]
     }
 
-    withName: 'CONCAT_MUTECT2.*' {
+    withName: 'MERGE_MUTECT2.*' {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
@@ -949,7 +936,7 @@ process{
     }
 
     //MANTA
-    withName: 'CONCAT_MANTA_SOMATIC' {
+    withName: 'MERGE_MANTA_SOMATIC' {
         ext.prefix       = {"${meta.id}.somatic_sv"}
     }
 
@@ -971,10 +958,10 @@ process{
     }
 
     //STRELKA
-    withName: 'CONCAT_STRELKA_INDELS' {
+    withName: 'MERGE_STRELKA_INDELS' {
         ext.prefix       = {"${meta.id}.somatic_indels"}
     }
-    withName: 'CONCAT_STRELKA_SNVS' {
+    withName: 'MERGE_STRELKA_SNVS' {
         ext.prefix       = {"${meta.id}.somatic_snvs"}
     }
 

modules.json

@@ -147,6 +147,9 @@
             "gatk4/mergemutectstats": {
                 "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
+            "gatk4/mergevcfs": {
+                "git_sha": "4199a05aeb0ec277d40cb112949bb85893310873"
+            },
             "gatk4/mutect2": {
                 "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
@@ -219,9 +222,6 @@
             "strelka/somatic": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
-            "tabix/bgzip": {
-                "git_sha": "37bf3936f3665483d070a5e0e0b314311032af7c"
-            },
             "tabix/bgziptabix": {
                 "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
             },