Description of feature
Bakta annotates genomes and writes a set of text-format output files (.embl, .faa, .ffn, .fna, .gbff, .gff3, .hypotheticals.tsv, .hypotheticals.faa, .tsv, .txt, .json), none of which are currently compressed by the bakta/bakta module. Several of these (.embl, .gbff, .fna, .ffn) can get large for bigger genomes/collections, and per the nf-core component review checklist, large outputs should be gzipped where the downstream tooling allows it.
We carry a local patch in nf-core/magmap that gzips all of Bakta's outputs (writing them into a ${prefix}/ subdirectory and running gzip ${prefix}/* at the end of the script), used across a run that maps against potentially large genome collections where the annotation output volume adds up. Flagging this as a candidate for the upstream module rather than keeping it local-only, in case it's useful more broadly. Happy to open a PR with the change if that's welcome — wanted to check first since it changes the output paths/extensions. I suppose this could be controlled by a value argument to the module.
Description of feature
Bakta annotates genomes and writes a set of text-format output files (
.embl,.faa,.ffn,.fna,.gbff,.gff3,.hypotheticals.tsv,.hypotheticals.faa,.tsv,.txt,.json), none of which are currently compressed by thebakta/baktamodule. Several of these (.embl,.gbff,.fna,.ffn) can get large for bigger genomes/collections, and per the nf-core component review checklist, large outputs should be gzipped where the downstream tooling allows it.We carry a local patch in nf-core/magmap that gzips all of Bakta's outputs (writing them into a
${prefix}/subdirectory and runninggzip ${prefix}/*at the end of the script), used across a run that maps against potentially large genome collections where the annotation output volume adds up. Flagging this as a candidate for the upstream module rather than keeping it local-only, in case it's useful more broadly. Happy to open a PR with the change if that's welcome — wanted to check first since it changes the output paths/extensions. I suppose this could be controlled by a value argument to the module.