vcf sort fixed

uclahs-cds · Aug 10, 2023 · 8816004 · 8816004
1 parent 836db28
commit 8816004
Show file tree

Hide file tree

Showing 2 changed files with 20 additions and 4 deletions.
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
@@ -39,7 +39,7 @@ process intersect_VCFs_BCFtools {
     path "isec-1-or-more/*.txt", emit: isec
 
     script:
-    vcf_list = vcfs.toSortedList().join(' ')
+    vcf_list = vcfs.join(' ')
     regions_command = params.use_intersect_regions ? "--regions-file ${intersect_regions}" : ""
     """
     set -euo pipefail
@@ -97,7 +97,7 @@ process concat_VCFs_BCFtools {
     path ".command.*"
 
     script:
-    vcf_list = vcfs.toSortedList().flatten().join(' ')
+    vcf_list = vcfs.join(' ')
     """
     set -euo pipefail
     # BCFtools concat to create a single VCF with all nfiles +2 variants

diff --git a/module/intersect.nf b/module/intersect.nf
@@ -15,8 +15,16 @@ workflow intersect {
     script_dir_ch
 
     main:
+        vcfs_ch = tool_vcfs
+            .map {
+                it.sort { a, b ->
+                def toolA = file(a).getName()
+                def toolB = file(b).getName()
+                return toolA.compareTo(toolB)
+                }
+            } 
         intersect_VCFs_BCFtools(
-            tool_vcfs,
+            vcfs_ch,
             tool_indices,
             params.intersect_regions,
             params.intersect_regions_index
@@ -25,8 +33,16 @@ workflow intersect {
             script_dir_ch,
             intersect_VCFs_BCFtools.out.isec,
             )
+        consensus_vcfs_ch = intersect_VCFs_BCFtools.out.consensus_vcf
+            .map {
+                it.sort { a, b ->
+                def toolA = file(a).getName()
+                def toolB = file(b).getName()
+                return toolA.compareTo(toolB)
+                }
+            } 
         concat_VCFs_BCFtools(
-            intersect_VCFs_BCFtools.out.consensus_vcf,
+            consensus_vcfs_ch,
             intersect_VCFs_BCFtools.out.consensus_idx
             )
         compress_index_VCF(concat_VCFs_BCFtools.out.concat_vcf