A CGP workflow to generate checksum of an interleaved fastq

Workflow: A CGP workflow to generate checksum of an interleaved fastq

Fetched 2019-10-20 17:24:42 GMT

Verified with cwltool version 1.0.20180525185854

A workflow to generate checksums of FastQ files and a interleaved FastQ from them. See the [workflow-seq-import](https://github.com/cancerit/workflow-seq-import) website for more information.

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Nested Workflows
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Inputs/Outputs

This workflow is Open Source and may be reused according to the terms of: GNU Affero General Public License v3.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Doc
fastq_in	File	The gzipped interleaved fastq file to import.
put_address	String (Optional)	Optional PUT address to send JSON results of checksums
put_headers	String[] (Optional)	Optional headers to send with JSON results

Steps

ID	Runs	Label	Doc
in_chksum	https://raw.githubusercontent.com/cancerit/dockstore-cgp-chksum/0.4.1/Dockstore.cwl (CommandLineTool)	CGP file checksum generator	![build_status](https://quay.io/repository/wtsicgp/dockstore-cgp-chksum/status) A Docker container for producing file md5sum and sha512sum. See the [dockstore-cgp-chksum](https://github.com/cancerit/dockstore-cgp-chksum) website for more information.
manifest_string_to_file	toolkit/string_to_file.cwl (CommandLineTool)
if_input_is_bz2_generate_md5sum_else_return_input_chksum_json	toolkit/if_input_is_bz2_generate_md5sum_else_return_input_chksum_json.cwl (Workflow)	If Input file 1 has bz2 extension generate md5sum from input file 2 else returns input chksum json
if_input_is_bz2_convert_to_gz_else_just_rename	toolkit/if_input_is_bz2_convert_to_gz_else_just_rename.cwl (CommandLineTool)
results_manifest_string	toolkit/results_manifest.cwl (ExpressionTool)

Outputs

ID	Type	Label	Doc
interleaved_fastq_out	File
results_manifest	File
chksum_json	File
chksum_put_server_response	File (Optional)