🔧 ensure samtools split uses cram ref if cram ref given

kids-first · Aug 22, 2022 · 95c6003 · 95c6003
1 parent 637e33f
commit 95c6003
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/subworkflows/kfdrc_process_bam.cwl b/subworkflows/kfdrc_process_bam.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 id: kfdrc_process_bam
 requirements:
@@ -27,7 +27,9 @@ steps:
     run: ../tools/samtools_split.cwl
     in:
       input_bam: input_bam
-      reference: indexed_reference_fasta
+      reference:
+        source: [cram_reference, indexed_reference_fasta]
+        pickValue: first_non_null
     out: [bam_files] #+1 Nesting File[]
 
   realign_split_bam:

diff --git a/workflows/kfdrc_sentieon_alignment_wf.cwl b/workflows/kfdrc_sentieon_alignment_wf.cwl
@@ -277,7 +277,9 @@ steps:
     scatter: [input_bam]
     in:
       input_bam: input_bam_list
-      reference: untar_reference/indexed_fasta
+      reference: 
+        source: [cram_reference, untar_reference/indexed_fasta]
+        pickValue: first_non_null
       max_memory: samtools_split_max_memory
       cores: samtools_split_cores
     out: [bam_files]