From 80edc41f30dcc8a04f9462b9a7f58ae737f96267 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Fri, 22 May 2020 13:06:10 +0000
Subject: [PATCH 1/1] Adding gather cwls Arvados-DCO-1.1-Signed-off-by: Sarah
 Wait Zaranek <swz@curii.com> no issue #

---
 cwl/helper/gather-vcf-try2.cwl                | 57 ++++++++++++++++++
 cwl/helper/gather-vcf.cwl                     | 58 +++++++++++++++++++
 .../{old => not-in-use}/bwa-gatk-wf.cwl       |  0
 .../{ => not-in-use}/bwamem-samtools-sort.cwl |  0
 cwl/helper/{ => not-in-use}/calc-coverage.cwl |  0
 cwl/helper/{ => not-in-use}/check-sam.cwl     |  0
 cwl/helper/{ => not-in-use}/fix-groups.cwl    |  0
 .../{ => not-in-use}/samtools-fixmate.cwl     |  0
 .../{old => not-in-use}/samtools-sort.cwl     |  0
 9 files changed, 115 insertions(+)
 create mode 100644 cwl/helper/gather-vcf-try2.cwl
 create mode 100644 cwl/helper/gather-vcf.cwl
 rename cwl/helper/{old => not-in-use}/bwa-gatk-wf.cwl (100%)
 rename cwl/helper/{ => not-in-use}/bwamem-samtools-sort.cwl (100%)
 rename cwl/helper/{ => not-in-use}/calc-coverage.cwl (100%)
 rename cwl/helper/{ => not-in-use}/check-sam.cwl (100%)
 rename cwl/helper/{ => not-in-use}/fix-groups.cwl (100%)
 rename cwl/helper/{ => not-in-use}/samtools-fixmate.cwl (100%)
 rename cwl/helper/{old => not-in-use}/samtools-sort.cwl (100%)

diff --git a/cwl/helper/gather-vcf-try2.cwl b/cwl/helper/gather-vcf-try2.cwl
new file mode 100644
index 0000000..4bd8cf0
--- /dev/null
+++ b/cwl/helper/gather-vcf-try2.cwl
@@ -0,0 +1,57 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Gathering vcf using Picard 
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  DockerRequirement:
+    dockerPull: broadinstitute/gatk:4.1.7.0
+  ShellCommandRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.gvcf1)
+      - $(inputs.gvcf2)
+
+hints:
+  ResourceRequirement:
+    ramMin: 20000
+    coresMin: 4    
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+
+inputs:
+  gvcf1:
+    type: File
+  gvcf2:
+    type: File
+  sample: string
+  reference:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+outputs:
+  gatheredgvcf:
+    type: File
+    outputBinding:
+      glob: "*g.vcf.gz"
+
+baseCommand: /gatk/gatk
+
+arguments:
+  - "--java-options"
+  - "-Xmx8G" 
+  - MergeVcfs
+  - prefix: "-I"
+    valueFrom: $(inputs.gvcf1.basename) 
+  - prefix: "-I"
+    valueFrom: $(inputs.gvcf2.basename)
+  - prefix: "-O"
+    valueFrom: $(inputs.sample)g.vcf.gz
diff --git a/cwl/helper/gather-vcf.cwl b/cwl/helper/gather-vcf.cwl
new file mode 100644
index 0000000..7bba8a9
--- /dev/null
+++ b/cwl/helper/gather-vcf.cwl
@@ -0,0 +1,58 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Gathering vcf using Picard 
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  DockerRequirement:
+    dockerPull: broadinstitute/gatk:4.1.7.0
+  ShellCommandRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.gvcflist)
+      - $(inputs.gvcf1)
+      - $(inputs.gvcf2)
+
+hints:
+  ResourceRequirement:
+    ramMin: 20000
+    coresMin: 4    
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+
+inputs:
+  gvcf1:
+    type: File
+  gvcf2:
+    type: File
+  gvcflist:
+    type: File
+  sample: string
+  reference:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+outputs:
+  gatheredgvcf:
+    type: File
+    outputBinding:
+      glob: "*g.vcf.gz"
+
+baseCommand: /gatk/gatk
+
+arguments:
+  - "--java-options"
+  - "-Xmx8G" 
+  - GatherVcfs
+  - prefix: "-I"
+    valueFrom: $(inputs.gvcflist.basename) 
+  - prefix: "-O"
+    valueFrom: $(inputs.sample)g.vcf.gz
diff --git a/cwl/helper/old/bwa-gatk-wf.cwl b/cwl/helper/not-in-use/bwa-gatk-wf.cwl
similarity index 100%
rename from cwl/helper/old/bwa-gatk-wf.cwl
rename to cwl/helper/not-in-use/bwa-gatk-wf.cwl
diff --git a/cwl/helper/bwamem-samtools-sort.cwl b/cwl/helper/not-in-use/bwamem-samtools-sort.cwl
similarity index 100%
rename from cwl/helper/bwamem-samtools-sort.cwl
rename to cwl/helper/not-in-use/bwamem-samtools-sort.cwl
diff --git a/cwl/helper/calc-coverage.cwl b/cwl/helper/not-in-use/calc-coverage.cwl
similarity index 100%
rename from cwl/helper/calc-coverage.cwl
rename to cwl/helper/not-in-use/calc-coverage.cwl
diff --git a/cwl/helper/check-sam.cwl b/cwl/helper/not-in-use/check-sam.cwl
similarity index 100%
rename from cwl/helper/check-sam.cwl
rename to cwl/helper/not-in-use/check-sam.cwl
diff --git a/cwl/helper/fix-groups.cwl b/cwl/helper/not-in-use/fix-groups.cwl
similarity index 100%
rename from cwl/helper/fix-groups.cwl
rename to cwl/helper/not-in-use/fix-groups.cwl
diff --git a/cwl/helper/samtools-fixmate.cwl b/cwl/helper/not-in-use/samtools-fixmate.cwl
similarity index 100%
rename from cwl/helper/samtools-fixmate.cwl
rename to cwl/helper/not-in-use/samtools-fixmate.cwl
diff --git a/cwl/helper/old/samtools-sort.cwl b/cwl/helper/not-in-use/samtools-sort.cwl
similarity index 100%
rename from cwl/helper/old/samtools-sort.cwl
rename to cwl/helper/not-in-use/samtools-sort.cwl
-- 
2.30.2