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sanger-tol / genomenote

This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.
https://pipelines.tol.sanger.ac.uk/genomenote
MIT License
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Remove `bedtools_sort` #51

Closed priyanka-surana closed 1 year ago

priyanka-surana commented 1 year ago

Description of the bug

Currently the bedtools_bamtobed module includes bedtools_sort, which consumes a lot of memory. Considering removing the sort step and implementing with the basic linux sort Bedtools recommends sort -k 1,1 -k2,2n a.bed Currently the bed_sort step after bedtools_bamtobed run sort -k4, so these need to be combined, before filtering.