Adding modified code to select variants and gather arrays

[arvados-tutorial.git] / cwl / helper / samtools-sort.cwl

diff --git a/cwl/helper/samtools-sort.cwl b/cwl/helper/samtools-sort.cwl
index b583f66be91d2897efb58f3da911793e9cd3c4c7..02072cdfbf863e0e6f982cd7cb21bb33603a21e2 100644 (file)
--- a/cwl/helper/samtools-sort.cwl
+++ b/cwl/helper/samtools-sort.cwl
@@ -10,9 +10,6 @@ requirements:
   DockerRequirement:
     dockerPull: curii/bwa-samtools-picard
   ShellCommandRequirement: {}
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
   ResourceRequirement:
     ramMin: 20000
     coresMin: 4
@@ -27,7 +24,7 @@ inputs:
   sample: string
 
 outputs:
-  bam:
+  sortedbam:
     type: File
     outputBinding:
       glob: "*sorted.bam"
@@ -38,7 +35,7 @@ arguments:
   - sort
   - -@
   - $(runtime.cores)
-  - $(inputs.bam.basename)
+  - $(inputs.bam.path)
   - -m
   - '2G'
   - -o