open_pipelines
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epigen
Pipelines for NGS data preprocessing by the Bock lab and friends
Hello epigen, I am a wetlab cellbiologist with beginner to intermediate coding skills and I am trying setup the CROP-seq pipeline in our laboratory. They use looper and also the...
I made mistakes in merging commits (forgot to pull before making changes) and reverting. This pull request backtracks to when it was still running and pep2 compatible). Sorry!
After macs2 sambamba is called as defined in atacseq.yaml, but the nex sambamba view command is simply calling "sambamba": macs2 callpeak -t .... sambamba-0.7.1 depth region -t .... sambamba view...
in my fresh install (using the latest piper/loopercli) `self.prj['metadata']['output_dir']` was undefined resulting in a `TypeError: 'NoneType' object has no attribute '__getitem__'` I replaced it with the line of code that...
This should ease the requirement to use the pipelines with looper (through the sample yaml). Passed arguments in command line should overwride any passed in the sample yaml if this...
ATAC-seq pipeline exit if no mitochondrial reads are duplicated due to zero division error - see logfile: File "/Users/christianschmidl/src/open_pipelines/pipelines/atacseq.py", line 359, in parse_duplicate_stats prefix + "duplicate_percentage": (float(duplicates) / (single_ends +...
`atacseq.py` and `chipseq.py` should use functions from `pypiper.ngstk`. Specifically, this is in regard to `bam_to_bigwig` / `bamToBigWig` (though it may also apply to other pipeline-defined functions). At least from quick...
It looks like some pipelines, e.g. `chipseq.py`, are defined as command-line programs in `setup.py`. There it has an underscored name while in the `description` to the argument parser, the name...