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blast-scatter-flow-needs-work.cwl
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blast-scatter-flow-needs-work.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
InlineJavascriptRequirement: {}
StepInputExpressionRequirement: {}
ScatterFeatureRequirement: {}
id: blast_flow
label: blast-flow
inputs:
dir: string
tarball: string
scripts_dir: string?
split_script: string
worker_script: string
output_script: string
output_err_script: string
output_dir: string?
workers: string[]
outputs: []
steps:
ch_tar2dir:
in:
dir: dir
tarball: tarball
out:
[image]
run: ./ch-donttar2dir.cwl
blast_split:
in:
scripts_dir: scripts_dir
output_dir: output_dir
image: ch_tar2dir/image
split_script: split_script
system:
default: '--'
cc_flags:
default: '--no-home'
out:
[split_done]
run: ./blast-split.cwl
blast_workers:
scatter: worker
in:
worker: workers
scripts_dir: scripts_dir
output_dir: output_dir
split_done: blast_split/split_done
image: ch_tar2dir/image
worker_script: worker_script
out: []
run: ./blast-worker.cwl
blast_output:
in:
scripts_dir: scripts_dir
output_dir: output_dir
image: ch_tar2dir/image
output_script: output_script
system:
default: '--'
cc_flags:
default: '--no-home'
out:
[output_done]
run: ./blast-output.cwl
blast_output_err:
in:
scripts_dir: scripts_dir
output_dir: output_dir
image: ch_tar2dir/image
output_err_script: output_err_script
system:
default: '--'
cc_flags:
default: '--no-home'
out:
[output_err_done]
run: ./blast-output-err.cwl
# ch_remove:
# in:
# image: ch_tar2dir/image
# rm_flags:
# default: '-rf'
# output_done: blast_output/output_done
# output_err_done: blast_output_err/output_err_done
# out: []
# run: ./ch-remove.cwl