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Split input fasta file, smartly #193

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chasemc opened this issue Oct 18, 2021 · 0 comments
Open

Split input fasta file, smartly #193

chasemc opened this issue Oct 18, 2021 · 0 comments
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enhancement New feature or request good first issue Good for newcomers

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@chasemc
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chasemc commented Oct 18, 2021

This might only be important with quite large metagenomes and even then probably will still not be the slow step even if uneven.
Currently, when running in parallel, the input contigs are naively split/chunked into x-number of files.
We had discussed before that it might be good to split contigs a bit more evenly into files based on contain length so that computation will be a bit more even later.

Relevant code:

seqkit \\
split \\
${fasta} \\
${options.args} \\
${options.args2} \\
-O outfolder

'seqkit_split_options' {
publish_by_meta = ['id']
args = "-p ${params.num_splits}"
args2 = "--two-pass"
}

@chasemc chasemc added enhancement New feature or request good first issue Good for newcomers labels Oct 18, 2021
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Labels
enhancement New feature or request good first issue Good for newcomers
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