Update to draft-3, add note about docker v1.10

common-workflow-library · Apr 18, 2016 · 920c6be · 920c6be
1 parent b48c6e7
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diff --git a/workflows/lobSTR/README b/workflows/lobSTR/README
@@ -11,7 +11,11 @@ To run locally, you may install the reference implementation of CWL:
 $ wget http://files.teamerlich.org/lobstr/v3/ref/lobSTR_v3.0.2_hg19_resource_bundle.tar.gz
 $ tar xvzf lobSTR_v3.0.2_hg19_resource_bundle.tar.gz
 
-3) Run the demo:
+3) Ensure your docker version is compatible with the Arvados image ( < 1.10 ):
+
+$ docker --version
+
+4) Run the demo:
 
 $ ./lobSTR-workflow.cwl lobSTR-demo.json
 

diff --git a/workflows/lobSTR/allelotype.cwl b/workflows/lobSTR/allelotype.cwl
@@ -5,6 +5,9 @@ class: CommandLineTool
 
 description: Run lobSTR allelotype classifier.
 
+requirements:
+ - class: InlineJavascriptRequirement
+
 inputs:
   - id: bam
     type: File
@@ -45,7 +48,7 @@ inputs:
     inputBinding:
       prefix: "--index-prefix"
       valueFrom: |
-          ${ return {"path": $self.path.match(/(.*)ref\.fasta/)[1], "class": "File"}; }
+          ${ return {"path": self.path.match(/(.*)ref\.fasta/)[1], "class": "File"}; }
 
     secondaryFiles:
       - ".amb"
@@ -55,19 +58,19 @@ inputs:
       - ".rbwt"
       - ".rpac"
       - ".rsa"
-      - ${return $self.replace(/(.*)ref\.fasta/, "$1chromsizes.tab")}
-      - ${return $self.replace(/(.*)ref\.fasta/, "$1mergedref.bed")}
-      - ${return $self.replace(/(.*)ref\.fasta/, "$1ref_map.tab")}
+      - ${return self.path.replace(/(.*)ref\.fasta/, "$1chromsizes.tab")}
+      - ${return self.path.replace(/(.*)ref\.fasta/, "$1mergedref.bed")}
+      - ${return self.path.replace(/(.*)ref\.fasta/, "$1ref_map.tab")}
 
 outputs:
   - id: vcf
     type: File
     outputBinding:
-      glob: $(job.output_prefix + '.vcf')
+      glob: $(inputs['output_prefix'] + '.vcf')
   - id: "#vcf_stats"
     type: File
     outputBinding:
-      glob: $(job.output_prefix + '.allelotype.stats')
+      glob: $(inputs['output_prefix'] + '.allelotype.stats')
 
 baseCommand: ["allelotype", "--command", "classify"]
 

diff --git a/workflows/lobSTR/lobSTR-tool.cwl b/workflows/lobSTR/lobSTR-tool.cwl
@@ -236,12 +236,12 @@ outputs:
   - id: bam
     type: File
     outputBinding:
-      glob: $(job.output_prefix + '.aligned.bam')
+      glob: $(inputs['output_prefix'] + '.aligned.bam')
 
   - id: bam_stats
     type: File
     outputBinding:
-      glob: $(job.output_prefix + '.aligned.stats')
+      glob: $(inputs['output_prefix'] + '.aligned.stats')
 
 baseCommand: ["lobSTR"]
 arguments:

diff --git a/workflows/lobSTR/lobSTR-workflow.cwl b/workflows/lobSTR/lobSTR-workflow.cwl
@@ -47,19 +47,19 @@ inputs:
 outputs:
   - id: bam
     type: File
-    source: "#samindex.bam_with_bai"
+    source: "#samindex/bam_with_bai"
 
   - id: bam_stats
     type: File
-    source: "#lobSTR.bam_stats"
+    source: "#lobSTR/bam_stats"
 
   - id: vcf
     type: File
-    source: "#allelotype.vcf"
+    source: "#allelotype/vcf"
 
   - id: vcf_stats
     type: File
-    source: "#allelotype.vcf_stats"
+    source: "#allelotype/vcf_stats"
 
 hints:
   - class: DockerRequirement

diff --git a/workflows/lobSTR/samtools-sort.cwl b/workflows/lobSTR/samtools-sort.cwl
@@ -49,7 +49,7 @@ outputs:
   - id: output_file
     type: File
     outputBinding:
-      glob: $(job['output_name'])
+      glob: $(inputs['output_name'])
 
 baseCommand: ["samtools", "sort"]