From 92172b0bceb7af669a8dd09cea04c93e041dfe2e Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Wed, 17 Jun 2020 18:17:25 +0000
Subject: [PATCH] Updating links to "helper" cwl Arvados-DCO-1.1-Signed-off-by:
 Sarah Wait Zaranek <swz@curii.com> no issue #

---
 .../.scatter-gatk-wf-with-interval.cwl.swp    | Bin 12288 -> 0 bytes
 WGS-processing/cwl/helper/bwa-gatk-wf.cwl     |  65 ------------------
 .../cwl/helper/bwamem-gatk-report-wf.cwl      |  12 ++--
 .../cwl/helper/gatk-wf-with-interval.cwl      |   8 +--
 WGS-processing/cwl/helper/report-wf.cwl       |   6 +-
 WGS-processing/cwl/wgs-processing-wf.cwl      |   2 +-
 6 files changed, 14 insertions(+), 79 deletions(-)
 delete mode 100644 WGS-processing/cwl/helper/.scatter-gatk-wf-with-interval.cwl.swp
 delete mode 100644 WGS-processing/cwl/helper/bwa-gatk-wf.cwl

diff --git a/WGS-processing/cwl/helper/.scatter-gatk-wf-with-interval.cwl.swp b/WGS-processing/cwl/helper/.scatter-gatk-wf-with-interval.cwl.swp
deleted file mode 100644
index 6973e8cc94c9851ec8dc8dbb4908a04331c0d92c..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/WGS-processing/cwl/helper/bwa-gatk-wf.cwl b/WGS-processing/cwl/helper/bwa-gatk-wf.cwl
deleted file mode 100644
index 56c1758..0000000
--- a/WGS-processing/cwl/helper/bwa-gatk-wf.cwl
+++ /dev/null
@@ -1,65 +0,0 @@
-cwlVersion: v1.1
-class: Workflow
-
-requirements:
-  - class: SubworkflowFeatureRequirement
-
-inputs:
-  fastq1: File
-  fastq2: File
-  reference:
-    type: File
-    secondaryFiles:
-      - .amb
-      - .ann
-      - .bwt
-      - .pac
-      - .sa
-      - .fai
-      - ^.dict
-  sample: string
-
-outputs:
-  qc-html:
-    type: File[]
-    outputSource: fastqc/out-html
-  qc-zip:
-    type: File[]
-    outputSource: fastqc/out-zip 
-  vcf:
-    type: File
-    outputSource: haplotypecaller/vcf
-
-steps:
-  fastqc:
-    run: fastqc.cwl
-    in:
-      fastq1: fastq1
-      fastq2: fastq2
-    out: [out-html, out-zip]
-  bwamem-samtools-view:
-    run: bwamem-samtools-view.cwl
-    in:
-      fastq1: fastq1
-      fastq2: fastq2
-      reference: reference
-      sample: sample
-    out: [bam]
-  samtools-sort:
-    run: samtools-sort.cwl
-    in:
-      bam: bwamem-samtools-view/bam
-      sample: sample
-    out: [out]
-  samtools-index:
-    run: samtools-index.cwl
-    in:
-      bam: samtools-sort/out
-    out: [out]
-  haplotypecaller:
-    run: gatk-haplotypecaller.cwl
-    in:
-      reference: reference
-      bam: samtools-index/out
-      sample: sample
-    out: [vcf]
diff --git a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
index 0a4b9d2..f601e95 100644
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -43,7 +43,7 @@ outputs:
     outputSource: generate-report/report
 steps:
   fastqc:
-    run: fastqc.cwl
+    run: ./helper/fastqc.cwl
     in:
       fastq1: fastq1
       fastq2: fastq2
@@ -57,13 +57,13 @@ steps:
       sample: sample
     out: [bam]
   samtools-sort:
-    run: samtools-sort.cwl 
+    run: ./helper/samtools-sort.cwl 
     in:
       bam: bwamem-samtools-view/bam
       sample: sample
     out: [sortedbam]
   mark-duplicates:
-    run: mark-duplicates.cwl
+    run: ./helper/mark-duplicates.cwl
     in:
       bam: samtools-sort/sortedbam
     out: [dupbam,dupmetrics]
@@ -73,7 +73,7 @@ steps:
       bam: mark-duplicates/dupbam
     out: [indexedbam]
   haplotypecaller:
-    run: scatter-gatk-wf-with-interval.cwl 
+    run: ./helper/scatter-gatk-wf-with-interval.cwl 
     in:
       reference: reference
       bam: samtools-index/indexedbam
@@ -82,7 +82,7 @@ steps:
       knownsites1: knownsites
     out: [gatheredgvcf]
   generate-report:
-    run: report-wf.cwl
+    run: ./helper/report-wf.cwl
     in:
       gvcf: haplotypecaller/gatheredgvcf
       samplename: sample
@@ -90,4 +90,4 @@ steps:
       reportfunc: reportfunc
       headhtml: headhtml
       tailhtml: tailhtml
-    out: [report]  
+    out: [report] 
diff --git a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
index 4e9f456..c7bd802 100644
--- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@ -34,7 +34,7 @@ outputs:
 
 steps:
   basecalibrator:
-    run: gatk-baserecalibrator-with-interval.cwl
+    run: ./helper/gatk-baserecalibrator-with-interval.cwl
     in:
       bam: bam
       reference: reference
@@ -43,7 +43,7 @@ steps:
       intervallist: intervallist
     out: [recaltable]
   applyBQSR:
-    run: gatk-applyBSQR-with-interval.cwl
+    run: ./helper/gatk-applyBSQR-with-interval.cwl
     in: 
       reference: reference
       bam: bam
@@ -52,7 +52,7 @@ steps:
       recaltable: basecalibrator/recaltable
     out: [recalbam]
   haplotypecaller:
-    run: gatk-haplotypecaller-with-interval.cwl
+    run: ./helper/gatk-haplotypecaller-with-interval.cwl
     in:
       reference: reference
       bam: applyBQSR/recalbam
@@ -60,7 +60,7 @@ steps:
       intervallist: intervallist
     out: [gvcf]
   selectvariants:
-    run: gatk-selectvariants.cwl
+    run: ./helper/gatk-selectvariants.cwl
     in: 
       gvcf: haplotypecaller/gvcf
       reference: reference
diff --git a/WGS-processing/cwl/helper/report-wf.cwl b/WGS-processing/cwl/helper/report-wf.cwl
index de8ab3f..3403ebb 100644
--- a/WGS-processing/cwl/helper/report-wf.cwl
+++ b/WGS-processing/cwl/helper/report-wf.cwl
@@ -22,21 +22,21 @@ outputs:
 
 steps:
   gvcf-to-vcf:
-    run: gvcf-to-vcf.cwl
+    run: ./helper/gvcf-to-vcf.cwl
     in:
       gvcf: gvcf
       samplename: samplename
     out: [vcf]
 
   annotate:
-    run: annotate-vcf.cwl
+    run: ./helper/annotate-vcf.cwl
     in:
       vcf: gvcf-to-vcf/vcf
       clinvarvcf: clinvarvcf
     out: [reporttxt]
 
   generate-report:
-    run: generate-report.cwl
+    run: ./helper/generate-report.cwl
     in:
       reportfunc: reportfunc
       sampletxt: annotate/reporttxt
diff --git a/WGS-processing/cwl/wgs-processing-wf.cwl b/WGS-processing/cwl/wgs-processing-wf.cwl
index f7d2d00..e43bfe5 100644
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.1
+Version: v1.1
 class: Workflow
 
 requirements:
-- 
2.30.2