Bugfix .bai secondary file for ApplyBSQR behavior

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
index 52413a6ea4958dd60c2d433ee1af308decb9b0b8..f6d625a09c117a97f43d431cbbe6a02f8de3c94b 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
@@ -54,7 +54,7 @@ outputs:
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
     secondaryFiles:
-      - .bai
+      - ^.bai
     outputBinding:
       glob: "*nodups_BQSR.bam"
 

diff --git a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
index 4b3d1a79fc809fbdecccf1cd2da6b17617311680..0b6c1029ddc3f135ec39fbb834587906f336ffe3 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
@@ -25,7 +25,7 @@ inputs:
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
     secondaryFiles:
-      - .bai
+      - ^.bai
   reference:
     type: File
     format: edam:format_1929 # FASTA