Devel

aligner/sbg-alignment-cwl/steps/align.cwl

@@ -20,16 +20,16 @@ inputs:
     inputBinding:
       position: 9
       shellQuote: false
-  - 'sbg:toolDefaultValue': '14000'
+  - default: 14000
+    'sbg:toolDefaultValue': '14000'
     id: ram_min
     type: int?
     label: Minimum amount of RAM
-    default: 14000
-  - 'sbg:toolDefaultValue': '8'
+  - default: 8
+    'sbg:toolDefaultValue': '8'
     id: cores_min
     type: int?
     label: Minimum number of cores
-    default: 8
 outputs:
   - id: cram
     type: File?
@@ -198,6 +198,3 @@ requirements:
             else
                 return files.reverse();
         };
-hints:
-  - class: 'sbg:AWSInstanceType'
-    value: c5.4xlarge;ebs-gp2;512

aligner/sbg-alignment-cwl/steps/alignment-validation.cwl

@@ -34,16 +34,16 @@ inputs:
     label: Reference
     doc: Reference genome sequence.
     'sbg:fileTypes': 'FASTA, FA'
-  - 'sbg:toolDefaultValue': '7500'
+  - default: 2000
+    'sbg:toolDefaultValue': '7500'
     id: ram_min
     type: int?
     label: Minimum amount of RAM
-    default: 2000
-  - 'sbg:toolDefaultValue': '8'
+  - default: 1
+    'sbg:toolDefaultValue': '2'
     id: cores_min
     type: int?
     label: Minimum number of cores
-    default: 1
 outputs:
   - id: stdout
     label: stdout
@@ -92,9 +92,8 @@ requirements:
     coresMin: $(inputs.cores_min)
   - class: DockerRequirement
     dockerPull: 'statgen/alignment:1.0.0'
-  - class: InlineJavascriptRequirement
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.cram)
       - $(inputs.reference)
-
+  - class: InlineJavascriptRequirement

aligner/sbg-alignment-cwl/steps/post-align.cwl

@@ -18,23 +18,25 @@ inputs:
   - id: alignment_files
     type: 'File[]'
     'sbg:fileTypes': BAM
-  - id: threads
+  - default: 1
+    id: threads
     type: int?
     label: Number of threads
-    default: 1
   - id: input_cram
     type: File
     label: Input CRAM
     doc: Input CRAM is passed to Post-align for output naming.
     'sbg:fileTypes': CRAM
-  - id: ram_min
+  - default: 7500
+    'sbg:toolDefaultValue': '7500'
+    id: ram_min
     type: int?
     label: Minimum amount of RAM
-    default: 7500
-  - id: cores_min
+  - default: 8
+    'sbg:toolDefaultValue': '2'
+    id: cores_min
     type: int?
     label: Minimum number of cores
-    default: 8
 outputs:
   - id: output
     type: File?
@@ -113,7 +115,8 @@ requirements:
   - class: DockerRequirement
     dockerPull: 'statgen/alignment:1.0.0'
   - class: InitialWorkDirRequirement
-    listing: |-
+    listing:
+      - |-
         ${ 
             var out = []
             out.push(inputs.reference)
@@ -125,6 +128,3 @@ requirements:
 
         }
   - class: InlineJavascriptRequirement
-hints:
-  - class: 'sbg:AWSInstanceType'
-    value: m5.large;ebs-gp2;700

aligner/sbg-alignment-cwl/steps/pre-align.cwl

@@ -24,21 +24,21 @@ inputs:
     type: File
     label: Reference for output CRAM compressing
     'sbg:fileTypes': 'FASTA, FA'
-  - 'sbg:toolDefaultValue': '1'
+  - default: 1
+    'sbg:toolDefaultValue': '1'
     id: threads
     type: int?
     label: Number of threads
-    default: 1
-  - 'sbg:toolDefaultValue': '7500'
+  - default: 7500
+    'sbg:toolDefaultValue': '7500'
     id: ram_min
     type: int?
     label: Minimum amount of RAM
-    default: 7500
-  - 'sbg:toolDefaultValue': '8'
+  - default: 8
+    'sbg:toolDefaultValue': '2'
     id: cores_min
     type: int?
     label: Minimum number of cores
-    default: 8
 outputs:
   - id: fastq
     type: 'File[]?'
@@ -160,6 +160,3 @@ requirements:
             }
             return o1;
         };
-hints:
-  - class: 'sbg:AWSInstanceType'
-    value: m5.large;ebs-gp2;512

aligner/sbg-alignment-cwl/steps/samtools-sort.cwl

@@ -18,18 +18,20 @@ inputs:
     inputBinding:
       position: 4
       shellQuote: false
-  - id: threads
+  - default: 1
+    id: threads
     type: int?
     label: Number of threads
-    default: 1
-  - id: ram_min
+  - default: 7000
+    'sbg:toolDefaultValue': '7500'
+    id: ram_min
     type: int?
     label: Minimum amount of RAM
-    default: 7000
-  - id: cores_min
+  - default: 2
+    'sbg:toolDefaultValue': '2'
+    id: cores_min
     type: int?
     label: Minimum number of cores
-    default: 2
 outputs:
   - id: output
     type: File?
@@ -101,6 +103,3 @@ requirements:
             }
             return o1;
         };
-hints:
-  - class: 'sbg:AWSInstanceType'
-    value: c5.4xlarge;ebs-gp2;512

aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl

@@ -91,9 +91,6 @@ steps:
     label: Validation
     'sbg:x': 30
     'sbg:y': -107
-hints:
-  - class: 'sbg:AWSInstanceType'
-    value: c4.4xlarge;ebs-gp2;256
 requirements:
   - class: SubworkflowFeatureRequirement
 'dct:creator':

aligner/sbg-alignment-cwl/topmed-alignment.cwl

@@ -3,9 +3,9 @@ cwlVersion: v1.0
 id: topmed_alignment
 doc: >-
   A CWL wrapper of the TopMed alignment workflow described here:
-  https://github.com/statgen/docker-alignment
-  Tool Author: Hyun Min Kang (hmkang@umich.edu) and Adrian Tan (atks@umich.edu)
-  Wrapper Author: Marko Zecevic (marko.zecevic@sbgenomics.com)
+  https://github.com/statgen/docker-alignment Tool Author: Hyun Min Kang
+  (hmkang@umich.edu) and Adrian Tan (atks@umich.edu) Wrapper Author: Marko
+  Zecevic (marko.zecevic@sbgenomics.com)
 label: TOPMed Alignment
 $namespaces:
   sbg: 'https://sevenbridges.com'
@@ -45,13 +45,28 @@ inputs:
     label: Number of threads
   - id: ram_min
     type: int?
-    label: Minimum amount of RAM
+    label: Minimum amount of RAM - pre-align/sort/post-align
+    'sbg:x': -90.64398956298828
+    'sbg:y': 270.19915771484375
   - id: cores_min
     type: int?
-    label: Minimum number of cores
+    label: Minimum number of cores - pre-align/sort/post-align
+    'sbg:x': -47.17603302001953
+    'sbg:y': -313.5997314453125
+  - id: cores_min_1
+    type: int?
+    label: Minimum number of cores - alignment
+    'sbg:x': 10.978857040405273
+    'sbg:y': -417.4698791503906
+  - id: ram_min_1
+    type: int?
+    label: Minimum amount of RAM - alignment
+    'sbg:x': -40.91050720214844
+    'sbg:y': 391.3500061035156
 outputs:
   - id: output
-    outputSource: topmed_post_align/output
+    outputSource:
+      - topmed_post_align/output
     'sbg:fileTypes': CRAM
     type: File?
     label: Output CRAM file
@@ -67,21 +82,21 @@ steps:
       - id: comp_ref
         source: reference_genome
       - id: threads
-        source: threads
         default: 1
+        source: threads
       - id: ram_min
-        source: ram_min
         default: 7500
+        source: ram_min
       - id: cores_min
+        default: 2
         source: cores_min
-        default: 8
     out:
       - id: fastq
       - id: list
     run: steps/pre-align.cwl
     label: Pre-align 1.0
-    'sbg:x': 130.828125
-    'sbg:y': 0
+    'sbg:x': 150.79986572265625
+    'sbg:y': -54.310768127441406
   - id: topmed_align
     in:
       - id: reference
@@ -91,11 +106,11 @@ steps:
       - id: list
         source: topmed_pre_align/list
       - id: ram_min
-        source: ram_min
         default: 14000
+        source: ram_min_1
       - id: cores_min
-        source: cores_min
         default: 8
+        source: cores_min_1
     out:
       - id: cram
     run: steps/align.cwl
@@ -112,14 +127,14 @@ steps:
       - id: input_file
         source: topmed_align/cram
       - id: threads
-        source: threads
         default: 1
+        source: threads
       - id: ram_min
+        default: 7500
         source: ram_min
-        default: 7000
       - id: cores_min
-        source: cores_min
         default: 2
+        source: cores_min
     out:
       - id: output
     run: steps/samtools-sort.cwl
@@ -136,18 +151,19 @@ steps:
       - id: dbsnp
         source: dbsnp
       - id: alignment_files
-        source: samtools_sort/output
-      - id: input_cram
-        source: input_file
+        source:
+          - samtools_sort/output
       - id: threads
-        source: threads
         default: 1
+        source: threads
+      - id: input_cram
+        source: input_file
       - id: ram_min
-        source: ram_min
         default: 7500
+        source: ram_min
       - id: cores_min
+        default: 2
         source: cores_min
-        default: 8
     out:
       - id: output
     run: steps/post-align.cwl
@@ -159,7 +175,6 @@ hints:
     value: '8'
 requirements:
   - class: ScatterFeatureRequirement
-  - class: MultipleInputFeatureRequirement
 'dct:creator':
   'foaf:mbox': 'mailto:support@sbgenomics.com'
   'foaf:name': Seven Bridges