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sanger-tol / genomenote

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.
https://pipelines.tol.sanger.ac.uk/genomenote
MIT License
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Local module: genome_filter #4

Closed priyanka-surana closed 2 years ago

priyanka-surana commented 2 years ago

Description of feature

Software/tool: cut, sed

Function: Filter the genome index file

Current command:

cmd(qq[cut -f1,2 $ref_index | sed 's/-/_/g'|sort -k2,2 -nr > $$self{outdir}/$$self{hname}.genome])
priyanka-surana commented 2 years ago

I intend to handle this similar to #3. Write a bash script that takes the genome index from samtools/faidx and filters it.