Modularized configs and readable code structure

Clinical-Genomics-Lund / SomaticPanelPipeline

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Closed ramsainanduri closed 8 months ago

ramsainanduri commented 9 months ago

created custom configs for each subworkflow along with the module specific
added separate variables for frequency cutoff for variant calling in the hopper config
removed cnvkit old process from modules/local/cnvkit and all the respective files
removed ASCAT module
removed process 'ASCAT2SCARHRD, ASCAT2OVAHRDSCAR' from modules/local/hrdsw
removed stub block for Check csv (because it is not required)
GATK CNVs related process are now executed on a condition when gatk_cnv is set to true

ramsainanduri commented 9 months ago

All profiles were executed without errors

ramsainanduri commented 9 months ago

Git ready, folks, this commit is so massive, my apologies for the coding rampage.

ramsainanduri commented 8 months ago

Only SPP entry point is tested with four profiles

ViktorHy commented 8 months ago

OK, we still need to fix the other entry-points so that they use similar input csvs as the main entrypoint. We could merge this now

ramsainanduri commented 8 months ago

Merging it