Closed muffato closed 1 year ago
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)
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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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