removing unnecessary step, renaming cwl file

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
new file mode 100644 (file)
index 0000000..18ad65c
--- /dev/null
+++ b/cwl/bwamem-samtools-sort.cwl
@@ -0,0 +1,67 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Realigning fastqs and converting output to bam
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  DockerRequirement:
+    dockerPull: curii/bwa-samtools-picard
+  ShellCommandRequirement: {}
+  ResourceRequirement:
+    ramMin: 26000
+    coresMin: 16 
+
+hints:
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+
+inputs:
+  reference:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+  fastq1: File
+  fastq2: File
+  sample: string
+
+stdout: $(inputs.sample).bam
+
+outputs:
+  bam:
+    type: File
+    outputBinding:
+      glob: "*bam"
+
+arguments:
+  - /bwa-0.7.17/bwa
+  - mem
+  - -M
+  - -t
+  - $(runtime.cores)
+  - $(inputs.reference)
+  - -R
+  - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' 
+  - -c
+  - '250'
+  - $(inputs.fastq1)
+  - $(inputs.fastq2)
+  - shellQuote: false
+    valueFrom: '|'
+  - samtools
+  - sort 
+  - -@
+  - $(runtime.cores)
+  - -m
+  - '2G'
+  - -l
+  - '6'
+  - -o
+  - $(inputs.sample).sorted.bam

diff --git a/cwl/bwamem-samtools-view.cwl b/cwl/bwamem-samtools-view-org.cwl
similarity index 99%
rename from cwl/bwamem-samtools-view.cwl
rename to cwl/bwamem-samtools-view-org.cwl
index efc423e27db676afea44d840a826cff7e7584c51..689bf393906ccbb5e50353db21d4e6d53a236ca0 100644 (file)
--- a/cwl/bwamem-samtools-view.cwl
+++ b/cwl/bwamem-samtools-view-org.cwl
@@ -50,7 +50,7 @@ arguments:
   - -R
   - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' 
   - -c
   - -R
   - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' 
   - -c

-  - 250
+  - '250'

   - $(inputs.fastq1)
   - $(inputs.fastq2)
   - shellQuote: false
   - $(inputs.fastq1)
   - $(inputs.fastq2)
   - shellQuote: false

diff --git a/cwl/gatk-haplotypecaller.cwl b/cwl/gatk-haplotypecaller.cwl
index 9679d2af48df4ba1a117a102d2b72ae889dec41d..1169f451eb127bffeb412c15b9fd3e811a123074 100644 (file)
--- a/cwl/gatk-haplotypecaller.cwl
+++ b/cwl/gatk-haplotypecaller.cwl
@@ -8,7 +8,7 @@ $namespaces:
 
 requirements:
   DockerRequirement:
 
 requirements:
   DockerRequirement:

-    dockerPull: broadinstitute/gatk
+    dockerPull: broadinstitute/gatk:4.1.7.0

   InitialWorkDirRequirement:
     listing:
       - $(inputs.bam)
   InitialWorkDirRequirement:
     listing:
       - $(inputs.bam)

diff --git a/cwl/mark-duplicates.cwl b/cwl/mark-duplicates.cwl
index 8cdbb9b1cde3ddaebff0a965971f7eccd6c981a9..3d7cba6fa17d2a208e75fdaeabe83361dfe02dfd 100644 (file)
--- a/cwl/mark-duplicates.cwl
+++ b/cwl/mark-duplicates.cwl
@@ -7,7 +7,7 @@ $namespaces:
 
 requirements:
   DockerRequirement:
 
 requirements:
   DockerRequirement:

-    dockerPull: broadinstitute/gatk
+    dockerPull: broadinstitute/gatk:4.1.7.0

 
 hints:
   ResourceRequirement:
 
 hints:
   ResourceRequirement: