Workflow: CGP checksum and interleaved fastq generation workflow for a paired fastq

Fetched 2021-06-17 03:05:51 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.

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

Inputs

ID Type Title Doc
fastq_in File[]

Gzipped fastq files to import.

put_address https://w3id.org/cwl/salad#null[]

PUT address to send JSON results of checksums, use list of empty strings if no PUT is required.

put_headers String[] (Optional)

Optional headers to send with JSON results.

Steps

ID Runs Label Doc
manifest_string_to_file
string_to_file.cwl (CommandLineTool)
rename
rename.cwl (CommandLineTool)
interleave
cgp-seqval-qc_pairs.cwl (CommandLineTool)
CGP sequence validator

![build_status](https://quay.io/repository/wtsicgp/dockstore-cgp-seqval/status) A Docker container for validating interleaved fastq files.

See the dockstore-cgp-seqval [README](https://github.com/cancerit/dockstore-cgp-seqval/blob/develop/README.md) for full details of how to use.

input_chksum
https://raw.githubusercontent.com/cancerit/dockstore-cgp-chksum/0.4.0/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.

results_manifest_string
results_manifest.cwl (ExpressionTool)
output_chksum
https://raw.githubusercontent.com/cancerit/dockstore-cgp-chksum/0.4.0/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.

Outputs

ID Type Label Doc
results_manifest File
interleaved_fastq_out File (Optional) [FASTQ]
chksum_json File[] [JSON]
chksum_put_server_response https://w3id.org/cwl/salad#null[]
Permalink: https://w3id.org/cwl/view/git/38dc146b2282c0d6b0c4efe1aaae53236b68f969/cwls/chksum_seqval_wf_paired_fq.cwl