Merge pull request #1100 from maxulysse/deepvariant_intervals

FIX: Deepvariant duplicate index

CHANGELOG.md

@@ -22,6 +22,7 @@ Vuoinesluobbalah is a lake close to Bierikjávrre.
 - [#1089](https://github.com/nf-core/sarek/pull/1089) - Remove duplicated code
 - [#1093](https://github.com/nf-core/sarek/pull/1093) - Fixing Ascat by reverting meta.id in channels allele_files, loci_files, gc_file and rt_file to baseName.
 - [#1098](https://github.com/nf-core/sarek/pull/1098) - Fix Channel issue in Mutect2 subworkflow [#1094](https://github.com/nf-core/sarek/pull/1094)
+- [#1100](https://github.com/nf-core/sarek/pull/1100) - Remove duplicate index with deepvariant when no_intervals [#1069](https://github.com/nf-core/sarek/pull/1069)
 
 ## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure
 

conf/modules/deepvariant.config

@@ -22,7 +22,7 @@ process {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
-            pattern: "*vcf.gz",
+            pattern: "*{vcf.gz,vcf.gz.tbi}",
             saveAs: { meta.num_intervals > 1 ? null : "deepvariant/${meta.id}/${it}" }
         ]
     }
@@ -40,12 +40,4 @@ process {
         ext.prefix       = {"${meta.id}.deepvariant.g"}
     }
 
-    withName : 'TABIX_VC_DEEPVARIANT_.*' {
-        ext.prefix       = {"${meta.id}.deepvariant"}
-        publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/deepvariant/${meta.id}/" },
-            pattern: "*tbi"
-        ]
-    }
 }

subworkflows/local/bam_variant_calling_deepvariant/main.nf

@@ -1,8 +1,6 @@
 include { GATK4_MERGEVCFS as MERGE_DEEPVARIANT_GVCF } from '../../../modules/nf-core/gatk4/mergevcfs/main'
 include { GATK4_MERGEVCFS as MERGE_DEEPVARIANT_VCF  } from '../../../modules/nf-core/gatk4/mergevcfs/main'
 include { DEEPVARIANT                               } from '../../../modules/nf-core/deepvariant/main'
-include { TABIX_TABIX as TABIX_VC_DEEPVARIANT_GVCF  } from '../../../modules/nf-core/tabix/tabix/main'
-include { TABIX_TABIX as TABIX_VC_DEEPVARIANT_VCF   } from '../../../modules/nf-core/tabix/tabix/main'
 
 // Deepvariant: https://github.com/google/deepvariant/issues/510
 workflow BAM_VARIANT_CALLING_DEEPVARIANT {
@@ -44,10 +42,6 @@ workflow BAM_VARIANT_CALLING_DEEPVARIANT {
     MERGE_DEEPVARIANT_GVCF(gvcf_to_merge, dict)
     MERGE_DEEPVARIANT_VCF(vcf_to_merge, dict)
 
-    // Only when no_intervals
-    TABIX_VC_DEEPVARIANT_GVCF(gvcf_out.no_intervals)
-    TABIX_VC_DEEPVARIANT_VCF(vcf_out.no_intervals)
-
     // Mix intervals and no_intervals channels together
     gvcf = Channel.empty().mix(MERGE_DEEPVARIANT_GVCF.out.vcf, gvcf_out.no_intervals)
         // add variantcaller to meta map and remove no longer necessary field: num_intervals
@@ -61,8 +55,6 @@ workflow BAM_VARIANT_CALLING_DEEPVARIANT {
     versions = versions.mix(DEEPVARIANT.out.versions)
     versions = versions.mix(MERGE_DEEPVARIANT_GVCF.out.versions)
     versions = versions.mix(MERGE_DEEPVARIANT_VCF.out.versions)
-    versions = versions.mix(TABIX_VC_DEEPVARIANT_GVCF.out.versions)
-    versions = versions.mix(TABIX_VC_DEEPVARIANT_VCF.out.versions)
 
     emit:
     gvcf