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OpenOmics / chrom-seek

An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
https://openomics.github.io/chrom-seek/
MIT License
5 stars 2 forks source link

ppqt rule needs improved fix #19

Closed asyakhl closed 11 months ago

asyakhl commented 1 year ago

Currently using this code as a fix for ppqt rule to run the chrom-seek pipeline, but need to find a more straightforward solution.

 if paired_end:
    extensionsPPQT={"sorted": "bam", "Q5DD":"bam"}
else:
    extensionsPPQT= {"sorted": "bam", "tagAlign": "gz", "Q5DD": "tagAlign.gz"}
asyakhl commented 11 months ago

completed with 0ea11a6 commit