JetBrains-Research / washu

Reproducible and scalable technical pipelines for ChIP-Seq and RNA-Seq processing
https://artyomovlab.wustl.edu/aging
MIT License
0 stars 0 forks source link

Allow benchmark_consensus.sh use outliers.csv information #34

Closed iromeo closed 6 years ago

iromeo commented 6 years ago

At the moment benchmark_consesnus.sh was launched for folder which is manually created and cleaned from outliers e.g. /mnt/stripe/bio/experiments/configs/benchmark/benchmark/H3K27me3/macs_broad/clean/. It will be nice if we can do such cleanup automatically, without human factor. So I see 2 ways: 1) Do some cleanup script, which takes info from our current outliers.csv 2) Pass outliers.csv to benchmark_consesnus.sh so as allow it ignore outliers

iromeo commented 6 years ago

Also we have several tool related folders (zinbra, sicer, zinbra_noinput, macs2, ..), so we can pass this tool folder name to benchmark consensus script, instead of hardcoded folders

PetrTsurinov commented 6 years ago

Done via https://github.com/JetBrains-Research/washu/pull/43.