Sorted input files

nf-core · Jun 23, 2022 · 656af02 · 656af02
1 parent 9b8a96a
commit 656af02
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Showing 3 changed files with 16 additions and 16 deletions.
diff --git a/subworkflows/local/germline_variant_calling.nf b/subworkflows/local/germline_variant_calling.nf
@@ -18,14 +18,14 @@ workflow GERMLINE_VARIANT_CALLING {
         bwa                           // channel: [mandatory] bwa
         dbsnp                         // channel: [mandatory] dbsnp
         dbsnp_tbi                     // channel: [mandatory] dbsnp_tbi
-        known_sites
-        known_sites_tbi
         dict                          // channel: [mandatory] dict
         fasta                         // channel: [mandatory] fasta
         fasta_fai                     // channel: [mandatory] fasta_fai
         intervals                     // channel: [mandatory] intervals/target regions
         intervals_bed_gz_tbi          // channel: [mandatory] intervals/target regions index zipped and indexed
         intervals_bed_combined        // channel: [mandatory] intervals/target regions in one file unzipped
+        known_sites
+        known_sites_tbi
         // joint_germline                // val: true/false on whether to run joint_germline calling, only works in combination with haplotypecaller at the moment
 
     main:

diff --git a/subworkflows/local/tumor_variant_calling.nf b/subworkflows/local/tumor_variant_calling.nf
@@ -16,21 +16,21 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
     take:
         tools                         // Mandatory, list of tools to apply
         cram_recalibrated             // channel: [mandatory] cram
+        bwa                           // channel: [optional] bwa
+        chr_files
         dbsnp                         // channel: [mandatory] dbsnp
         dbsnp_tbi                     // channel: [mandatory] dbsnp_tbi
         dict                          // channel: [mandatory] dict
         fasta                         // channel: [mandatory] fasta
         fasta_fai                     // channel: [mandatory] fasta_fai
+        germline_resource             // channel: [optional]  germline_resource
+        germline_resource_tbi         // channel: [optional]  germline_resource_tbi
         intervals                     // channel: [mandatory] intervals/target regions
         intervals_bed_gz_tbi          // channel: [mandatory] intervals/target regions index zipped and indexed
         intervals_bed_combined        // channel: [mandatory] intervals/target regions in one file unzipped
-        germline_resource             // channel: [optional]  germline_resource
-        germline_resource_tbi         // channel: [optional]  germline_resource_tbi
+        mappability
         panel_of_normals              // channel: [optional]  panel_of_normals
         panel_of_normals_tbi          // channel: [optional]  panel_of_normals_tbi
-        chr_files
-        mappability
-        bwa                           // channel: [optional] bwa
 
     main:
 

diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -792,35 +792,35 @@ workflow SAREK {
             [],
             dbsnp,
             dbsnp_tbi,
-            known_sites,
-            known_sites_tbi,
             dict,
             fasta,
             fasta_fai,
             intervals,
             intervals_bed_gz_tbi,
-            intervals_bed_combined)
+            intervals_bed_combined,
+            known_sites,
+            known_sites_tbi)
             // params.joint_germline)
 
         // TUMOR ONLY VARIANT CALLING
         TUMOR_ONLY_VARIANT_CALLING(
             params.tools,
             cram_variant_calling_tumor_only,
+            [],
+            chr_files,
             dbsnp,
             dbsnp_tbi,
             dict,
             fasta,
             fasta_fai,
+            germline_resource,
+            germline_resource_tbi,
             intervals,
             intervals_bed_gz_tbi,
             intervals_bed_combined,
-            germline_resource,
-            germline_resource_tbi,
-            pon,
-            pon_tbi,
-            chr_files,
             mappability,
-            []
+            pon,
+            pon_tbi
         )
 
         // PAIR VARIANT CALLING