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wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL
MIT License
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Exposing Variant Filtering Params #104

Closed Layth17 closed 10 months ago

Layth17 commented 1 year ago

Tumor VAF cutoff for FP filter applied to mutect and strelka calls can now be tuned at immuno.wdl level using immuno.min_var_freq in yaml.

immuno.varscan_min_var_freq is used specifically for varscan now.

immuno.filter_somatic_llr_threshold can be set at the level of immuno.wdl in yaml

Layth17 commented 1 year ago

unclear what the functional distinction between varscan_min_var_freq and min_var_freq for now ...

For now, immuno.varscan_min_var_freq can be set using YAML immuno.filter_somatic_llr_threshold as well

Layth17 commented 1 year ago

immuno.wdl takes in varscan_min_var_freq & min_var_freq then passes them to somatic_exome.wdl which passes them to detectVariants.wdl which passes min_var_freq for both subworkflows/mutect.wdl and subworkflows/strelka_and_post_processing.wdl (varscan_min_var_freq is used for the varscan process) and respectively pass that value to subworkflows.fp_filter.wdl which ultimately calls tools/fp_filters with that specified value.

malachig commented 1 year ago

I think we should reconsider why we are setting defaults for these cutoffs at various places in the chain from immuno -> somatic -> detect variants -> variant caller sub workflow -> variant caller tool or false positive filter itself.

I think we want the user running analysis from each of these points to be able override the default, but unless we are explicitly doing it on purpose for a good reason, why should we define a default value anywhere other than the final place it is about to be used (in this case either in varscan or the false positive filter)?

chrisamiller commented 1 year ago

Yeah, agree with Malachi. This seems like an opportunity to clean up some of this parameter passing//logic (see my comment inline upthread). It's gotten that way over time, through changes by lots of different folks, but we can draw a line in the sand and say "the mess stops now" :)

malachig commented 10 months ago

Working on testing but if all goes well this PR should be deprecated by:

https://github.com/wustl-oncology/analysis-wdls/pull/136

malachig commented 10 months ago

Testing of #136 worked out. Closing this one.