Updating bwamem CWL and adding base recalibrator cwl

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/cwl/bwamem-samtools-sort.cwl b/cwl/bwamem-samtools-sort.cwl
index 18ad65cee8db1cba0446f0f8d3d03a7a034b0dc8..2077ebde683d36af3d09abaf5960579ebdd61a72 100644 (file)
--- a/cwl/bwamem-samtools-sort.cwl
+++ b/cwl/bwamem-samtools-sort.cwl
@@ -10,12 +10,13 @@ requirements:
     dockerPull: curii/bwa-samtools-picard
   ShellCommandRequirement: {}
   ResourceRequirement:
-    ramMin: 26000
+    ramMin: 20000 
     coresMin: 16 
 
 hints:
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
+    keep_cache: 9216
 
 inputs:
   reference:
@@ -58,9 +59,9 @@ arguments:
   - samtools
   - sort 
   - -@
-  - $(runtime.cores)
+  - '16'
   - -m
-  - '2G'
+  - '500M'
   - -l
   - '6'
   - -o

diff --git a/cwl/gatk-baserecalibrator.cwl b/cwl/gatk-baserecalibrator.cwl
new file mode 100644 (file)
index 0000000..a5105e8
--- /dev/null
+++ b/cwl/gatk-baserecalibrator.cwl
@@ -0,0 +1,62 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Generating recalibration table for BQSR 
+
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  DockerRequirement:
+    dockerPull: broadinstitute/gatk:4.1.7.0
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.bam)
+
+hints:
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+    keep_cache: 1024
+  ResourceRequirement:
+    ramMin: 5000
+    coresMin: 2
+
+inputs:
+  bam:
+    type: File
+  reference:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+  sample: string
+  knownsites1: 
+    type: File
+    secondaryFiles:
+      - .tbi
+
+outputs:
+  recaltable:
+    type: File
+    outputBinding:
+      glob: "*.table"
+
+baseCommand: /gatk/gatk
+
+arguments:
+  - "--java-options"
+  - "-Xmx4G"
+  - BaseRecalibrator
+  - prefix: "-R"
+    valueFrom: $(inputs.reference)
+  - prefix: "-I"
+    valueFrom: $(inputs.bam.basename)
+  - prefix: "--known-sites"
+    valueFrom: $(inputs.knownsites1)
+  - prefix: "-O"
+    valueFrom: $(inputs.sample)_recal_data.table