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

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

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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Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title 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 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)
Permalink: https://w3id.org/cwl/view/git/4765cf6955bdce1320fdead7fe51be0e1b63c33d/cwls/chksum_seqval_wf_interleaved_fq.cwl