Add umicollapse as an alternative to umi-tools #1369
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TODO: - [ ] Benchmark paired ends mode - [ ] Include in multiqc
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Excellent work, clean and well-structured! I think, you found very smart solutions to not duplicate too much of the code.
Of course, we should wait for the lead developers of the pipeline to review as well prior to merging, but in general you have my support for this addition! Ideally, your fix for umicollapse would also be included in the form of an updated tool version.
Please don't forget the Changelog later and also to add your name to the contributors (well deserved)!
| @@ -30,6 +30,7 @@ params { | |||
| with_umi = false | |||
| skip_umi_extract = false | |||
| umitools_extract_method = 'string' | |||
| umi_dedup_tool = 'umicollapse' | |||
| umitools_grouping_method = 'directional' | |||
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Reading that makes we wonder if we should be conservative regarding the parameter names or make them more generic, e.g. renaming umitools_grouping_method to something like umi_grouping_method / umi_dedup_grouping_method etc.
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Yes, I thought about that too. Depends on your policy for introducing breaking changes between versions. If the authors are OK, I can rename these parameters to be more generic.
| @@ -30,6 +30,7 @@ params { | |||
| with_umi = false | |||
| skip_umi_extract = false | |||
| umitools_extract_method = 'string' | |||
| umi_dedup_tool = 'umicollapse' | |||
| umitools_grouping_method = 'directional' | |||
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Yes, I thought about that too. Depends on your policy for introducing breaking changes between versions. If the authors are OK, I can rename these parameters to be more generic.
Signed-off-by: Siddhartha Bagaria <[email protected]>
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I checked the output of UMICollapse, and it definitely does not follow the assumptions stated in prepare_for_rsem.py. So |
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@MatthiasZepper all remaining tasks are now done. Please take another look. |
Unfortunately, the UMICollapse module has not yet been upgraded... |
Checklist:
PREPARE_FOR_SALMONis needed