Cleiti
commented
1 year ago - demultiplex(.smk).py NOT prepping sarek anymore. Given to prep_sarek.py. Since separate script, now is based on files in demultiplexed/ instead of local vars
- sarek prep code totally changed to fit sarek 3.2.0 (which si DSL2)
- custom.config DELETED: process names not used anymore + and uppmax nfcore default config exists.
- added --save_mapped, -bg (background)
- added --tools deepvariant,vep (deepvariant confirmed best variantcaller, vep not confirmed)
- added --skip_tools baserecalibrator (don't seem to have any input for that)
- sarek_input.csv LANE set different for each sample(row) (all same "patient")
- deleted --clip_r1 6 --clip_r2 6 --three_prime_clip_r1 3 --three_prime_clip_r2 3 (options not in new sarek ver + doesn't seem to affect anything)