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| 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 <mooney@wustl.edu>
…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! 😄 |
jasonwalker80
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Yeah, I would definitely change the wording from redundant. They are ideally not redundant at all, but rather specific regions of interest at a specific level, ex. base, target, etc.
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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 |
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@jasonwalker80 @jhundal can you +1 content