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sbg · Jul 26, 2018 · 3184a92 · 3184a92
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commit 3184a92
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Showing 6 changed files with 35 additions and 28 deletions.
diff --git a/topmed-workflows/alignment/steps/align.cwl b/topmed-workflows/alignment/steps/align.cwl
@@ -190,4 +190,4 @@ requirements:
         };
 hints:
   - class: 'sbg:AWSInstanceType'
-    value: c4.4xlarge;ebs-gp2;512
+    value: c5.4xlarge;ebs-gp2;512
diff --git a/topmed-workflows/alignment/steps/post-align.cwl b/topmed-workflows/alignment/steps/post-align.cwl
@@ -10,7 +10,7 @@ inputs:
   - id: reference
     type: File
   - id: dbsnp
-    type: File
+    type: File?
     inputBinding:
       position: 3
       prefix: '--dbsnp'
@@ -21,11 +21,22 @@ inputs:
   - id: threads
     type: int?
     label: Number of threads
+  - id: input_cram
+    type: File
+    label: Input CRAM
+    doc: Input CRAM is passed to Post-align for output naming.
+    'sbg:fileTypes': CRAM
 outputs:
   - id: output
     type: File?
     outputBinding:
-      glob: '*cram'
+      glob: |-
+        ${
+          var outname = inputs.input_cram.path.split('/').slice(-1)[0]
+          outname = outname.split('.').slice(0, -1).join('.')
+          outname = outname.concat(".recab.cram")
+          return outname
+        }
 label: Post-align
 arguments:
   - position: 1
@@ -58,20 +69,10 @@ arguments:
     shellQuote: false
     valueFrom: |-
       ${
-        function sharedStart(array){
-          var A= array.concat().sort(), 
-          a1= A[0], a2= A[A.length-1], L= a1.length, i= 0;
-          while(i<L && a1.charAt(i)=== a2.charAt(i)) i++;
-          return a1.substring(0, i);
-        }
-        var path_list = []
-        inputs.alignment_files.forEach(function(f){return path_list.push(f.path.replace(/\\/g,'/').replace( /.*\//, '' ))})
-        var common_prefix = sharedStart(path_list)
-        if (common_prefix.length >0){
-          return common_prefix.concat(".recab.cram")
-        } else {
-          return "recab.cram"
-        }    
+        var outname = inputs.input_cram.path.split('/').slice(-1)[0]
+        outname = outname.split('.').slice(0, -1).join('.')
+        outname = outname.concat(".recab.cram")
+        return outname
       }
   - position: 0
     prefix: '--threads'
@@ -99,11 +100,13 @@ requirements:
   - class: ShellCommandRequirement
   - class: ResourceRequirement
     ramMin: 7500
-    coresMin: 8
+    coresMin: 2
   - class: DockerRequirement
     dockerPull: 'statgen/alignment:1.0.0'
   - class: InitialWorkDirRequirement
-    listing: |-
+    listing:
+      - $(inputs.input_cram)
+      - |-
         ${ 
             var out = []
             out.push(inputs.reference)
@@ -116,4 +119,4 @@ requirements:
   - class: InlineJavascriptRequirement
 hints:
   - class: 'sbg:AWSInstanceType'
-    value: c4.4xlarge;ebs-gp2;512
+    value: m5.large;ebs-gp2;700
diff --git a/topmed-workflows/alignment/steps/pre-align.cwl b/topmed-workflows/alignment/steps/pre-align.cwl
@@ -102,7 +102,7 @@ requirements:
   - class: ShellCommandRequirement
   - class: ResourceRequirement
     ramMin: 7500
-    coresMin: 8
+    coresMin: 2
   - class: DockerRequirement
     dockerPull: 'statgen/alignment:1.0.0'
   - class: InitialWorkDirRequirement
@@ -151,4 +151,4 @@ requirements:
         };
 hints:
   - class: 'sbg:AWSInstanceType'
-    value: c4.4xlarge;ebs-gp2;512
+    value: m5.large;ebs-gp2;512
diff --git a/topmed-workflows/alignment/steps/samtools-sort.cwl b/topmed-workflows/alignment/steps/samtools-sort.cwl
@@ -2,7 +2,7 @@ class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
   sbg: 'https://sevenbridges.com'
-id: marko_zecevic/topmed-alignment/samtools-sort/0
+id: marko_zecevic_topmed_alignment_samtools_sort_0
 baseCommand:
   - samtools
   - sort
@@ -91,4 +91,4 @@ requirements:
         };
 hints:
   - class: 'sbg:AWSInstanceType'
-    value: c4.4xlarge;ebs-gp2;512
+    value: c5.4xlarge;ebs-gp2;512
diff --git a/topmed-workflows/alignment/topmed-alignment-checker.cwl b/topmed-workflows/alignment/topmed-alignment-checker.cwl
@@ -1,6 +1,7 @@
 class: Workflow
 cwlVersion: v1.0
 id: topmed_alignment_checker
+doc: Checker for the TopMed alignment workflow.
 label: TOPMed Alignment - checker
 $namespaces:
   sbg: 'https://sevenbridges.com'
@@ -101,3 +102,4 @@ requirements:
 'dct:creator':
   'foaf:mbox': 'mailto:support@sbgenomics.com'
   'foaf:name': Seven Bridges
+'sbg:wrapperAuthor': Marko Zecevic ([email protected])
diff --git a/topmed-workflows/alignment/topmed-alignment.cwl b/topmed-workflows/alignment/topmed-alignment.cwl
@@ -12,8 +12,8 @@ inputs:
     'sbg:fileTypes': CRAM
     type: File
     label: Input CRAM file
-    'sbg:x': -233.1334991455078
-    'sbg:y': -43.2740478515625
+    'sbg:x': -253.4855499267578
+    'sbg:y': 25.186986923217773
   - id: bwa_index
     'sbg:fileTypes': TAR
     type: File
@@ -57,7 +57,7 @@ steps:
       - id: comp_ref
         source: reference_genome
       - id: threads
-        default: 8
+        default: 1
     out:
       - id: fastq
       - id: list
@@ -107,7 +107,9 @@ steps:
         source:
           - samtools_sort/output
       - id: threads
-        default: 8
+        default: 1
+      - id: input_cram
+        source: input_file
     out:
       - id: output
     run: steps/post-align.cwl