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common-workflow-library / legacy

Deprecated
https://github.com/common-workflow-library/bio-cwl-tools
Apache License 2.0
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Modifications to trimmomatic and STAR #150

Closed biokcb closed 6 years ago

biokcb commented 6 years ago

Corrected the following errors in these tools:

  1. trimmomatic.cwl did not collect paired-end trimmed-unpaired outputs due to file names being incorrect

  2. trimmomatic-illumina_clipping.yaml had only one optional input specified as optional. When keepBothReads is given, but minAdapterLength is not, it places a null value in the argument that doesn't work. Updated this and main trimmomatic.cwl documents to work with optional inputs per the trimmomatic manual. Alternatively instead of optional inputs & the many if else statements I placed in there you could set default values (minAdapterLength: 8 and keepBothReads: false). Not sure which is more acceptable, but the edits I've made work on my end.

  3. STAR did not have an output field for the marking duplicates in a bam option (--bamRemoveDuplicatesType) and did not run when --limitBAMsortRAM was a long int for larger memory requests.

biokcb commented 6 years ago

Sorry for the multiple commits - let me know if this should be split into different pull requests, I am still learning how to use GitHub and didn't realize I should have split them. Thanks. :)

mr-c commented 6 years ago

This is great @biokcb , thanks!

biokcb commented 6 years ago

Awesome, thanks for responding so quickly!