Merge pull request #994 from zlskidmore/master

fixed bug regarding missing indexed bam in bigwig
genome · Jan 20, 2021 · ecac0fd · ecac0fd
2 parents da335d9 + 5637ea5
commit ecac0fd
Show file tree

Hide file tree

Showing 4 changed files with 8 additions and 7 deletions.
diff --git a/definitions/pipelines/rnaseq.cwl b/definitions/pipelines/rnaseq.cwl
@@ -148,7 +148,7 @@ steps:
     stringtie:
         run: ../tools/stringtie.cwl
         in:
-            bam: mark_dup/sorted_bam
+            bam: index_bam/indexed_bam
             reference_annotation: reference_annotation
             sample_name: sample_name
             strand: strand

diff --git a/definitions/pipelines/rnaseq_star_fusion.cwl b/definitions/pipelines/rnaseq_star_fusion.cwl
@@ -183,7 +183,7 @@ steps:
     stringtie:
         run: ../tools/stringtie.cwl
         in:
-            bam: mark_dup/sorted_bam
+            bam: index_bam/indexed_bam
             reference_annotation: gtf_file
             sample_name: sample_name
             strand: strand
@@ -195,7 +195,7 @@ steps:
             refFlat: refFlat
             ribosomal_intervals: ribosomal_intervals
             strand: strand
-            bam: mark_dup/sorted_bam
+            bam: index_bam/indexed_bam
         out:
             [metrics, chart]
     bam_to_cram:
@@ -214,7 +214,7 @@ steps:
     cgpbigwig_bamcoverage:
         run: ../tools/bam_to_bigwig.cwl
         in:
-            bam: mark_dup/sorted_bam
+            bam: index_bam/indexed_bam
             reference: reference_fasta
         out:
             [outfile]
diff --git a/definitions/pipelines/rnaseq_star_fusion_with_xenosplit.cwl b/definitions/pipelines/rnaseq_star_fusion_with_xenosplit.cwl
@@ -237,7 +237,7 @@ steps:
     stringtie:
         run: ../tools/stringtie.cwl
         in:
-            bam: mark_dup/sorted_bam
+            bam: index_bam/indexed_bam
             reference_annotation: graft_gtf_file
             sample_name: sample_name
             strand: strand
@@ -249,13 +249,13 @@ steps:
             refFlat: refFlat
             ribosomal_intervals: ribosomal_intervals
             strand: strand
-            bam: mark_dup/sorted_bam
+            bam: index_bam/indexed_bam
         out:
             [metrics, chart]
     cgpbigwig_bamcoverage:
         run: ../tools/bam_to_bigwig.cwl
         in:
-            bam: mark_dup/sorted_bam
+            bam: index_bam/indexed_bam
             reference: reference
         out:
             [outfile]
diff --git a/definitions/tools/stringtie.cwl b/definitions/tools/stringtie.cwl
@@ -54,6 +54,7 @@ inputs:
         type: File
         inputBinding:
             position: 4
+        secondaryFiles: [.bai,^.bai]
 outputs:
     transcript_gtf:
         type: File