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chksum_for_a_corrupted_xam_file.cwl
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chksum_for_a_corrupted_xam_file.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
id: "chksum-corrupted-single-file-workflow"
label: "A CGP workflow to generate checksum and corruption info of a single file"
cwlVersion: v1.0
requirements:
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
xam_in:
type: File
doc: "input file"
put_address:
type: string?
doc: "Optional PUT address to send JSON results of checksums"
put_headers:
type: string[]?
doc: "Optional headers to send with JSON results."
corruption_status:
type: File
doc: "A JSON file of file corruption status"
outputs:
chksum_json:
type: File
outputSource: in_chksum/chksum_json
chksum_put_server_response:
type: ["null", File]
outputSource: in_chksum/server_response
results_manifest:
type: File
outputSource: manifest_string_to_file/outfile
steps:
in_chksum:
in:
in_file:
source: xam_in
put_address:
source: put_address
put_headers:
source: put_headers
ignore_all_curl_exits:
valueFrom: $(true)
out: [chksum_json, server_response]
run: https://raw.githubusercontent.com/cancerit/dockstore-cgp-chksum/0.4.1/Dockstore.cwl
results_manifest_string:
in:
input_files:
source: [xam_in]
linkMerge: merge_flattened
input_chksum_results:
source: [in_chksum/chksum_json]
linkMerge: merge_flattened
corruption_status:
source: corruption_status
out: [out_string]
run: results_manifest_for_corrupted_input.cwl
manifest_string_to_file:
in:
in_string:
source: [results_manifest_string/out_string]
out: [outfile]
run: string_to_file.cwl
doc: |
A workflow to generate checksums of a file and add info in corruption_status file into a JSON output. See the [workflow-seq-import](https://github.com/cancerit/workflow-seq-import) website for more information.
$schemas:
- https://schema.org/version/latest/schema.rdf
$namespaces:
s: http://schema.org/
s:codeRepository: https://github.com/cancerit/workflow-seq-import
s:license: https://spdx.org/licenses/AGPL-3.0
s:author:
- class: s:Person
s:email: mailto:yyaobo@gmail.com
s:name: Yaobo Xu
dct:creator:
foaf:name: Yaobo Xu
foaf:mbox: "genservhelp@sanger.ac.uk"