Merge pull request #520 from maxulysse/dev_annotation

Clean up annotation
nf-core · Apr 14, 2022 · 3b1543d · 3b1543d
2 parents 5000c94 + 07cc13e
commit 3b1543d
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Showing 5 changed files with 20 additions and 13 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -976,7 +976,7 @@ if (params.tools && (params.tools.contains('vep'))) {
 
 if (params.tools && (params.tools.contains('merge'))) {
     process {
-        withName: 'NFCORE_SAREK:SAREK:ANNOTATE:MERGE_ANNOTATE:ANNOTATION_BGZIPTABIX' {
+        withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_MERGE:ANNOTATION_BGZIPTABIX' {
             ext.prefix       = {"${meta.id}_snpEff_VEP.ann.vcf"}
         }
     }

diff --git a/subworkflows/local/annotate.nf b/subworkflows/local/annotate.nf
@@ -2,9 +2,9 @@
 // ANNOTATION
 //
 
-include { ANNOTATION_SNPEFF                       } from '../nf-core/annotation/snpeff/main'
-include { ANNOTATION_ENSEMBLVEP as MERGE_ANNOTATE } from '../nf-core/annotation/ensemblvep/main'
-include { ANNOTATION_ENSEMBLVEP                   } from '../nf-core/annotation/ensemblvep/main'
+include { ANNOTATION_SNPEFF                         } from '../nf-core/annotation/snpeff/main'
+include { ANNOTATION_ENSEMBLVEP as ANNOTATION_MERGE } from '../nf-core/annotation/ensemblvep/main'
+include { ANNOTATION_ENSEMBLVEP                     } from '../nf-core/annotation/ensemblvep/main'
 
 workflow ANNOTATE {
     take:
@@ -32,11 +32,11 @@ workflow ANNOTATE {
 
     if (tools.contains('merge')) {
         vcf_ann_for_merge = ANNOTATION_SNPEFF.out.vcf_tbi.map{ meta, vcf, tbi -> [meta, vcf] }
-        MERGE_ANNOTATE(vcf_ann_for_merge, vep_genome, vep_species, vep_cache_version, vep_cache)
+        ANNOTATION_MERGE(vcf_ann_for_merge, vep_genome, vep_species, vep_cache_version, vep_cache)
 
-        ch_reports  = ch_reports.mix(MERGE_ANNOTATE.out.reports)
-        ch_vcf_ann  = ch_vcf_ann.mix(MERGE_ANNOTATE.out.vcf_tbi)
-        ch_versions = ch_versions.mix(MERGE_ANNOTATE.out.versions.first())
+        ch_reports  = ch_reports.mix(ANNOTATION_MERGE.out.reports)
+        ch_vcf_ann  = ch_vcf_ann.mix(ANNOTATION_MERGE.out.vcf_tbi)
+        ch_versions = ch_versions.mix(ANNOTATION_MERGE.out.versions.first())
     }
 
     if (tools.contains('vep')) {

diff --git a/subworkflows/nf-core/annotation/ensemblvep/main.nf b/subworkflows/nf-core/annotation/ensemblvep/main.nf
diff --git a/subworkflows/nf-core/annotation/snpeff/main.nf b/subworkflows/nf-core/annotation/snpeff/main.nf
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -184,9 +184,7 @@ include { TUMOR_ONLY_VARIANT_CALLING                     } from '../subworkflows
 include { PAIR_VARIANT_CALLING                           } from '../subworkflows/local/pair_variant_calling'
 
 // Annotation
-include { ANNOTATE                                       } from '../subworkflows/local/annotate' addParams(
-    annotation_cache:                  params.annotation_cache
-)
+include { ANNOTATE                                       } from '../subworkflows/local/annotate'
 
 // REPORTING VERSIONS OF SOFTWARE USED
 include { CUSTOM_DUMPSOFTWAREVERSIONS                    } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'