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Dockstore.cwl
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Dockstore.cwl
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#!/usr/bin/env cwl-runner
class: CommandLineTool
id: "dockstore-tool-runner"
label: "A Dockstore tool that can call download from Redwood, call another Dockstore tool, and then upload back to Redwood."
cwlVersion: v1.0
doc: |
A Docker container from which Dockstore containers may be launched.
```
Usage:
# fetch CWL
$> dockstore tool cwl --entry quay.io/ucsc_cgl/DockstoreRunner > Dockstore.cwl
# make a runtime JSON template and edit it
$> dockstore tool convert cwl2json --cwl Dockstore.cwl > Dockstore.json
# run it locally with the Dockstore CLI
$> dockstore tool launch --entry quay.io/ucsc_cgl/DockstoreRunner --json Dockstore.json
```
dct:creator:
'@id': http://orcid.org/0000-0002-7681-6415
foaf:name: Brian O'Connor
foaf:mbox: mailto:briandoconnor@gmail.com
requirements:
- class: DockerRequirement
dockerPull: "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.25"
hints:
- class: ResourceRequirement
coresMin: 1
ramMin: 4092
outdirMin: 512000
description: "the process requires at least 4G of RAM"
inputs:
program_name:
type: string
doc: "Program to be associated with the uploaded file"
inputBinding:
prefix: --program-name
redwood_token:
type: string
doc: "Token for storage client"
inputBinding:
prefix: --redwood-token
redwood_host:
type: string
doc: "Host for storage client"
inputBinding:
prefix: --redwood-host
json_encoded:
type: string
doc: "Encoded JSON for container to be run by Dockstore"
inputBinding:
prefix: --json-encoded
docker_uri:
type: string
doc: "Path to docker image from which to create container"
inputBinding:
prefix: --docker-uri
dockstore_url:
type: string
doc: "Path to docker image from which to create container"
inputBinding:
prefix: --dockstore-url
workflow_type:
type: string
doc: "String that describes the workflow type: [qc, sequence_upload, sequence_upload_qc_report, alignment, alignment_qc_report, rna_seq_quantification, germline_variant_calling, somatic_variant_calling, immuno_target_pipelines]"
inputBinding:
prefix: --workflow-type
launch_type:
type: string?
doc: "String that describes the launch type: tool or workflow"
inputBinding:
prefix: --launch-type
parent_uuids:
type: string
doc: "UUIDs for parent"
inputBinding:
prefix: --parent-uuids
tmpdir:
type: string
doc: "Path to the temporary directory where intermediate files are written"
inputBinding:
prefix: --tmpdir
vm_instance_type:
type: string
doc: "Instance type used."
inputBinding:
prefix: --vm-instance-type
vm_region:
type: string
doc: "Instance region."
inputBinding:
prefix: --vm-region
vm_location:
type: string
doc: "The cloud this VM is running in e.g. 'aws'."
inputBinding:
prefix: --vm-location
vm_instance_cores:
type: int
doc: "Instance cores."
inputBinding:
prefix: --vm-instance-cores
vm_instance_mem_gb:
type: int
doc: "Instance memory in GB as int."
inputBinding:
prefix: --vm-instance-mem-gb
outputs:
output_metadata_json:
type: File
outputBinding:
glob: metadata.json
doc: "Result metadata.json files from tool run on the host"
baseCommand: ["python", "/usr/local/bin/DockstoreRunner.py"]