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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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Unnecessary sort #45

Closed muffato closed 1 year ago

muffato commented 2 years ago

Description of the bug

Found whilst reviewing #44

In the contact_maps subworkflow, bedtools/bamtobed already sorts the bed file, cf https://github.com/sanger-tol/nf-core-modules/blob/main/modules/bedtools/bamtobed/main.nf#L28 There is no need to sort it again at https://github.com/sanger-tol/genomenote/blob/dev/subworkflows/local/contact_maps.nf#L41

(noticed that because bedtools/bamtobed takes a ton of memory)

Command used and terminal output

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Relevant files

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System information

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