Merge branch 'blog-examples'

refs #18178

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

diff --git a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
index cf9210cc2dca7078fe22e27cd0605cb27332db9f..f4a3ed1b141729de2b9c4ae0fa485a8dda47b80c 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
+++ b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
@@ -12,8 +12,8 @@ hints:
     keep_cache: 1024
     outputDirType: keep_output_dir
   ResourceRequirement:
-    ramMin: 50000
-    coresMin: 16
+    ramMin: 25000
+    coresMin: 8
   SoftwareRequirement:
     packages:
       BWA:

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