update ped filter subwf

nf-cmgg · nvnieuwk · Jan 27, 2025 · Jan 22, 2025 · Jan 22, 2025 · Jan 23, 2025
commit 5af2749a0b3e2ea6b0f15e2627d502eab51d7c17
diff --git a/conf/modules.config b/conf/modules.config
@@ -236,7 +236,7 @@ process {
 
     withName: "^.*GERMLINE:BCFTOOLS_NORM\$" {
         ext.prefix = {"${meta.id}.normalized"}
-        ext.args = "-m-"
+        ext.args = "-m- --output-type z --write-index=tbi"
     }
 
     /*
@@ -257,7 +257,7 @@ process {
 
     withName: "^.*VCF_PED_RTGTOOLS:BCFTOOLS_ANNOTATE\$" {
         ext.prefix = { "${meta.id}.${meta.caller}.ped.annotated" }
-        ext.args = "--output-type z"
+        ext.args = "--output-type z --write-index=tbi"
     }
 
     /*

diff --git a/subworkflows/local/vcf_ped_rtgtools/main.nf b/subworkflows/local/vcf_ped_rtgtools/main.nf
@@ -29,16 +29,19 @@ workflow VCF_PED_RTGTOOLS {
 
     def ch_annotate_input = ch_vcfs
         .join(RTGTOOLS_PEDFILTER.out.output, failOnDuplicate:true, failOnMismatch:true)
-        .map { meta, vcf, _tbi, ped_vcf ->
-            [ meta, vcf, [], [], [], ped_vcf ]
+        .map { meta, vcf, tbi, ped_vcf ->
+            [ meta, vcf, tbi, [], [], ped_vcf ]
         }
 
     BCFTOOLS_ANNOTATE(
         ch_annotate_input
     )
     ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions.first())
+
+    def ch_ped_vcfs = BCFTOOLS_ANNOTATE.out.vcf
+        .join(BCFTOOLS_ANNOTATE.out.tbi, failOnDuplicate:true, failOnMismatch:true)
 
     emit:
-    ped_vcfs = BCFTOOLS_ANNOTATE.out.vcf    // [ val(meta), path(vcf) ]
-    versions = ch_versions                  // [ path(versions) ]
+    ped_vcfs = ch_ped_vcfs  // [ val(meta), path(vcf), path(tbi) ]
+    versions = ch_versions  // [ path(versions) ]
 }
diff --git a/workflows/germline.nf b/workflows/germline.nf
@@ -574,13 +574,8 @@ workflow GERMLINE {
             )
             ch_versions = ch_versions.mix(BCFTOOLS_NORM.out.versions.first())
 
-            TABIX_NORMALIZE(
-                BCFTOOLS_NORM.out.vcf
-            )
-            ch_versions = ch_versions.mix(TABIX_NORMALIZE.out.versions.first())
-
             ch_normalized_variants = BCFTOOLS_NORM.out.vcf
-                .join(TABIX_NORMALIZE.out.tbi, failOnDuplicate:true, failOnMismatch:true)
+                .join(BCFTOOLS_NORM.out.tbi, failOnDuplicate:true, failOnMismatch:true)
         } else {
             ch_normalized_variants = ch_filtered_variants
         }
@@ -633,7 +628,6 @@ workflow GERMLINE {
         // Annotation of the variants and creation of Gemini-compatible database files
         //
 
-        def ch_annotation_output = Channel.empty()
         if (annotate) {
             VCF_ANNOTATION(
                 ch_ped_vcfs,
@@ -652,32 +646,11 @@ workflow GERMLINE {
             ch_versions = ch_versions.mix(VCF_ANNOTATION.out.versions)
             ch_reports  = ch_reports.mix(VCF_ANNOTATION.out.reports)
 
-            ch_annotation_output = VCF_ANNOTATION.out.annotated_vcfs
+            ch_final_vcfs = VCF_ANNOTATION.out.annotated_vcfs
         } else {
-            ch_annotation_output = ch_ped_vcfs
+            ch_final_vcfs = ch_ped_vcfs
         }
 
-        //
-        // Tabix the resulting VCF
-        //
-
-        def ch_ann_tabix = ch_annotation_output.branch { meta, vcf, tbi=[] ->
-            indexed: tbi
-                return [ meta, vcf, tbi ]
-            not_indexed: !tbi
-                return [ meta, vcf ]
-        }
-
-        TABIX_FINAL(
-            ch_ann_tabix.not_indexed
-        )
-        ch_versions = ch_versions.mix(TABIX_FINAL.out.versions.first())
-
-        ch_final_vcfs = ch_ann_tabix.indexed
-            .mix(
-                ch_ann_tabix.not_indexed.join(TABIX_FINAL.out.tbi, failOnDuplicate:true, failOnMismatch:true)
-            )
-
         //
         // Validate the found variants
         //