Star Fusion -- relaxing FFPM filter & extracting preliminary files

wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL

MIT License

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Star Fusion -- relaxing FFPM filter & extracting preliminary files #85

Closed Layth17 closed 1 year ago

Layth17 commented 1 year ago

https://github.com/STAR-Fusion/STAR-Fusion/wiki https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#string-interpolation

[x] Assign optional variable min_ffpm_level a default value of 0.05 unless otherwise specified
[x] Save 7 new preliminary files + 2 were already saved
[x] Extract all 9 files into rna_seq/star_fusion in ìmmuno.wdl`
[x] grouping

malachig commented 1 year ago

hi @Layth17 . I belive that if we want the end user to be able to set this new parameter to a new value then we also need this added to the inputs in immuno.wdl:

Float? min_ffpm_level = 0.05

malachig commented 1 year ago

My test runs with this PR have succeeded. The results are nicely organized and we now get the extra preliminary results files. The one file whose name depends on user choice of ffpm filter appears to get generated and capture correctly. I think we can merge this PR now.