Cellranger cwl

sub_workflows/cellranger_count_aggr.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "Cellranger count and aggr subworkflow."
+
+requirements:
+  - class: ScatterFeatureRequirement        
+
+inputs:
+    fastq_directory:
+        type: Directory[]
+    chemistry:
+        type: string?
+    reference:
+        type: Directory
+    sample_name:
+        type: string[]
+
+steps:
+  count:
+    run: /gscuser/matthewmosior/Software/cellranger_cwl/cellranger_count/tool/cellranger_count.cwl
+    scatter: [fastq_directory, sample_name]
+    scatterMethod: dotproduct
+    in:
+      chemistry: chemistry
+      fastq_directory: fastq_directory
+      reference: reference
+      sample_name: sample_name
+    out: [out_dir, molecule_info_file]
+  prepare_aggr_csv:
+    run: /gscuser/matthewmosior/Software/cellranger_cwl/prepare_aggr_csv/tool/prepare_aggr_csv.cwl
+    in:
+      out_dir: count/out_dir
+      molecule_h5: count/molecule_info_file
+    out:
+      [aggr_csv_file]
+  aggr:
+    run: /gscuser/matthewmosior/Software/cellranger_cwl/cellranger_aggr/tool/cellranger_aggr.cwl
+    in:
+      csv_file: prepare_aggr_csv/aggr_csv_file
+    out:
+      [aggr_out_dir]
+
+outputs:
+  count_out_dir:
+    type: Directory[]
+    outputSource: count/out_dir
+  count_molecule_file:
+    type: File[]
+    outputSource: count/molecule_info_file
+  aggr_out_dir:
+    type: Directory
+    outputSource: aggr/aggr_out_dir

tools/cellranger_aggr.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+label: "Run Cellranger Aggregate (aggr)."
+
+baseCommand: ["/opt/cellranger-3.0.1/cellranger","aggr"]
+arguments: ["--id=test_AGGR","--localcores=$(runtime.cores)", "--localmem=$(runtime.ram/1000)","--normalize=mapped"]
+
+requirements: 
+    - class: InlineJavascriptRequirement
+    - class: DockerRequirement
+      dockerPull: "registry.gsc.wustl.edu/mgi/cellranger:3.0.1"
+    - class: ResourceRequirement
+      ramMin: 64000
+      coresMin: 8
+
+inputs:
+    csv_file:
+        type: File
+        inputBinding:
+            prefix: --csv=
+            position: 1
+            separate: false
+        doc: "CSV file containing samples to be aggregated."
+
+outputs:
+    aggr_out_dir:
+        type: Directory
+        outputBinding:
+            glob: "/gscuser/matthewmosior/Software/cellranger_cwl/cellranger_aggr/test_AGGR" 

tools/cellranger_count.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+label: "Run Cell Ranger Count"
+
+baseCommand: ["/opt/cellranger-3.0.1/cellranger", "count"]
+arguments: ["--id=GEX_example", "--localcores=$(runtime.cores)", "--localmem=$(runtime.ram/1000)"]
+
+requirements:
+    - class: InlineJavascriptRequirement
+    - class: DockerRequirement
+      dockerPull: "registry.gsc.wustl.edu/mgi/cellranger:3.0.1"
+    - class: ResourceRequirement
+      ramMin: 56000
+      coresMin: 8
+
+inputs:
+    chemistry:
+        type: string?
+        inputBinding:
+            prefix: --chemistry=
+            position: 1
+            separate: false
+        default: "auto"
+        doc: "Assay configuration used, default 'auto' should usually work without issue"
+    fastq_directory:
+        type: Directory
+        inputBinding:
+           prefix: --fastqs=
+           position: 2
+           separate: false
+        doc: "Array of directories containing fastq files"
+    reference:
+        type: Directory
+        inputBinding:
+            prefix: --transcriptome=
+            position: 3
+            separate: false
+        doc: "Transcriptome reference compatible with input species and Cell Ranger"
+    sample_name:
+        type: string
+        inputBinding:
+            prefix: --sample=
+            position: 4
+            separate: false
+        doc: "Sample name, must be same as name specified in sample sheet in previous mkfastq step"
+
+outputs:
+    out_dir:
+        type: Directory
+        outputBinding:
+            glob: "$(inputs.sample_name)/outs/"
+    molecule_info_file:
+        type: File
+        outputBinding:
+            glob: "$(inputs.sample_name)/outs/molecule_info.h5"  

tools/prepare_aggr_csv.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+label: "Prepare csv file for cellranger aggr."
+baseCommand: ["/bin/bash","/gscuser/matthewmosior/Software/cellranger_cwl/prepare_aggr_csv/prepare_aggr_csv.sh"]
+requirements:
+    - class: InlineJavascriptRequirement
+    - class: ResourceRequirement
+      ramMin: 32000
+      coresMin: 12
+
+inputs:
+    out_dir:
+        type: Directory[]
+        inputBinding:
+            position: 1
+    molecule_h5:
+        type: File[]
+        inputBinding:
+            position: 2
+outputs:
+    aggr_csv_file:
+        type: File
+        outputBinding:
+            glob: "$(inputs.out_dir)_aggr.csv"