more docs for somatic exome #872
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| @@ -124,13 +124,25 @@ inputs: | |||
| In general for a WES exome reagent bait_intervals and target_intervals are the same. | |||
| per_base_intervals: | |||
| type: ../types/labelled_file.yml#labelled_file[] | |||
| label: "per_base_intervals: yaml file specifying name and input for picard CollectHsMetrics" | |||
| doc: | | |||
| Optional input, redundant with bait_intervals, provides a way to name name the output file from running picard CollectHsMetrics. See ../types/labelled_file.yml for an example. | |||
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In subworkflows/hs_metrics.cwl, the CollectHsMetrics tool runs multiple times with different options. It's not just a different filename; it's a different mode of running!
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Perhaps this would help: https://github.com/genome/analysis-workflows/wiki/Frequently-Asked-Questions-(FAQ)#somatic-exome
Co-Authored-By: Thomas B. Mooney <[email protected]>
…ows into somatic_exome_doc
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@tmooney Is this more what you had in mind, this is my understanding based on reading the cwl |
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@zlskidmore Yeah, something like that. I'd prefer to describe them as optional extra regions for further metric generation rather than "redundant". But at a minimum they are definitely not YAML files! 😄 |
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Hi @zlskidmore, this input doc sounds relevant with my recent PR each other. I wrote a doc for exome alignment and QC. |
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yeah, I you suggesting we merge PRs? |
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@zlskidmore - doing a little cleanup here. Did this get merged into gchang's PR, or otherwise included? Are there changes that still need to be made? I'm all for extra documentation - just wondering where this PR stands. Thanks! |
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I don't think it was ever merged, perhaps @gschang can verify, I never did a merge though |
@jasonwalker80 @jhundal can you +1 content