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genomic-medicine-sweden · May 28, 2024 · 843579f · 843579f
1 parent cda20e0
commit 843579f
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Showing 3 changed files with 5 additions and 43 deletions.
diff --git a/conf/modules/allele_specific_calling.config b/conf/modules/allele_specific_calling.config
@@ -47,23 +47,14 @@ process {
     withName: '.*ALLELE_SPECIFIC_CALLING:REMOVE_DUPLICATES' {
         ext.args = '--output-type z --rm-dup none'
         ext.prefix = { "${meta.id}_split_rmdup" }
-    }
-
-    withName: '.*ALLELE_SPECIFIC_CALLING:ADD_VARCALLER_TO_BED' {
-        ext.args2   = '-s 1 -b 2 -e 3'
-    }
-
-    withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_ANNOTATE' {
-        ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z"
-        ext.prefix = { "${meta.id}_split_rmdup_info" }
         publishDir = [
             path: { "${params.outdir}/bootstrapann" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
-    withName: '.*ALLELE_SPECIFIC_CALLING:TABIX_ANNOTATE' {
+    withName: '.*ALLELE_SPECIFIC_CALLING:TABIX_REMOVE_DUP' {
         publishDir = [
             path: { "${params.outdir}/bootstrapann" },
             mode: params.publish_dir_mode,

diff --git a/subworkflows/local/allele_specific_calling.nf b/subworkflows/local/allele_specific_calling.nf
@@ -28,9 +28,6 @@ workflow ALLELE_SPECIFIC_CALLING {
         ch_dict            // channel: [mandatory] [ val(meta), path(dict) ]
         ch_intervals       // channel: [mandatory] [ path(intervals) ]
         ch_case_info       // channel: [mandatory] [ val(case_info) ]
-        variant_caller     // parameter: [mandatory] default: 'bcftools'
-        ch_foundin_header  // channel: [mandatory] [ path(header) ]
-        ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ]
 
     main:
         ch_versions = Channel.empty()
@@ -111,27 +108,6 @@ workflow ALLELE_SPECIFIC_CALLING {
         REMOVE_DUPLICATES(ch_remove_dup_in, ch_fasta)
         TABIX_REMOVE_DUP(REMOVE_DUPLICATES.out.vcf)
 
-        ch_genome_chrsizes.flatten().map{chromsizes ->
-            return [[id:variant_caller], chromsizes]
-            }
-            .set { ch_varcallerinfo }
-
-        ADD_VARCALLER_TO_BED (ch_varcallerinfo).gz_tbi
-            .map{meta,bed,tbi -> return [bed, tbi]}
-            .set{ch_varcallerbed}
-
-        REMOVE_DUPLICATES.out.vcf
-            .join(TABIX_REMOVE_DUP.out.tbi)
-            .combine(ch_varcallerbed)
-            .combine(ch_foundin_header)
-            .set { ch_annotate_in }
-
-        BCFTOOLS_ANNOTATE(ch_annotate_in)
-
-        TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf)
-
-
-
         ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions.first())
         ch_versions = ch_versions.mix(BCFTOOLS_INDEX.out.versions.first())
         ch_versions = ch_versions.mix(GATK4_ASEREADCOUNTER.out.versions.first())
@@ -142,13 +118,11 @@ workflow ALLELE_SPECIFIC_CALLING {
         ch_versions = ch_versions.mix( TABIX_TABIX.out.versions.first() )
         ch_versions = ch_versions.mix( SPLIT_MULTIALLELICS.out.versions.first() )
         ch_versions = ch_versions.mix( TABIX_AFTER_SPLIT.out.versions.first() )
-        ch_versions = ch_versions.mix( ADD_VARCALLER_TO_BED.out.versions.first() )
+        ch_versions = ch_versions.mix( REMOVE_DUPLICATES.out.versions.first() )
         ch_versions = ch_versions.mix( TABIX_REMOVE_DUP.out.versions.first() )
-        ch_versions = ch_versions.mix( BCFTOOLS_ANNOTATE.out.versions.first() )
-        ch_versions = ch_versions.mix( TABIX_ANNOTATE.out.versions.first() )
 
     emit:
-        vcf      = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), [ path(vcf) ] ]
-        tbi      = TABIX_ANNOTATE.out.tbi    // channel: [ val(meta), [ path(tbi) ] ]
+        vcf      = REMOVE_DUPLICATES.out.vcf // channel: [ val(meta), [ path(vcf) ] ]
+        tbi      = TABIX_REMOVE_DUP.out.tbi    // channel: [ val(meta), [ path(tbi) ] ]
         versions = ch_versions               // channel: [ path(versions.yml) ]
 }
diff --git a/workflows/tomte.nf b/workflows/tomte.nf
@@ -177,10 +177,7 @@ workflow TOMTE {
         ch_references.fai,
         ch_references.sequence_dict,
         ch_references.interval_list,
-        ch_case_info,
-        params.variant_caller,
-        ch_foundin_header,
-        ch_references.chrom_sizes
+        ch_case_info
     )
     ch_versions = ch_versions.mix(ALLELE_SPECIFIC_CALLING.out.versions)