Workflow: A CGP workflow to generate checksum of an interleaved fastq
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.
- Selected
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- Default Values
- Nested Workflows
- Tools
- 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 | 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 |
 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