Lower RAM request by bwa to run on 9tee4

[arvados-tutorial.git] / WGS-processing / cwl / helper / bwamem-samtools-view.cwl

diff --git a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
index 0ad81840545acc43bcade1875b554fa0a4086859..f4a3ed1b141729de2b9c4ae0fa485a8dda47b80c 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
+++ b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
@@ -4,16 +4,16 @@ label: Align FASTQs with BWA
 
 requirements:
   DockerRequirement:
-    dockerPull: curii/bwa-samtools-picard
+    dockerPull: curii/bwa-samtools
   ShellCommandRequirement: {}
-  ResourceRequirement:
-    ramMin: 50000
-    coresMin: 16 
 
 hints:
   arv:RuntimeConstraints:
-    keep_cache: 1024 
+    keep_cache: 1024
     outputDirType: keep_output_dir
+  ResourceRequirement:
+    ramMin: 25000
+    coresMin: 8
   SoftwareRequirement:
     packages:
       BWA:
@@ -36,15 +36,15 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  fastq1: 
+  fastq1:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R1)
-  fastq2: 
+  fastq2:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R2)
-  sample: 
+  sample:
     type: string
     label: Sample Name
 
@@ -66,7 +66,7 @@ arguments:
   - $(runtime.cores)
   - $(inputs.reference)
   - -R
-  - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' 
+  - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
   - -c
   - '250'
   - $(inputs.fastq1)
@@ -91,6 +91,6 @@ $namespaces:
  arv: "http://arvados.org/cwl#"
  cwltool: "http://commonwl.org/cwltool#"
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl