updated module: xengsort/index - #12494
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| { assert path(process.out.hash[0][1]).exists() }, | ||
| { assert path(process.out.info[0][1]).exists() }, | ||
| { assert snapshot( | ||
| path(process.out.hash[0][1]).getFileName().toString(), | ||
| path(process.out.info[0][1]).getFileName().toString(), | ||
| process.out.findAll { key, val -> key.startsWith("versions") } |
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This could probably all be sanitizeOutput(process.out, unstableKeys: ["hash", "info"])
| def subtables = Math.max([(cpus / 2) as int - 1, cpus - 3, 19].min(), 1) | ||
| if ((subtables % 2) == 0) { | ||
| subtables += 1 | ||
| } | ||
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| def read_threads = Math.ceil(subtables / 10) as int | ||
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| def split_threads = 2 * read_threads | ||
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| if ((subtables + read_threads + split_threads) >= cpus) { | ||
| read_threads = 1 | ||
| split_threads = 2 | ||
| } |
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Where is all this coming from?
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@SPPearce any thoughts on this? Or should i omit this approach entirely?
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If it is in the source code, does that mean it does it automatically?
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I don't mind you doing this if that is suggested by the tool, just add a comment pointing to that effect
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If it is in the source code, does that mean it does it automatically?
This is the tools default threading behavior if none of --threads-split, --threads-read or --subtables is specified when executing the tool. Meaning these could be overwritten by a nextflow.config file.
Since the tool doesn't explicitly support a single --threads ${task.cpus} (or similar) logic, i figured this approach was still in line with nf-core modules guidelines and the support for multi-threading?
| description: The expression to obtain the version of the tool | ||
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| authors: | ||
| - "@diegomscoelho" |
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Still was the original author. You can add yourself though.
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Updated existing
xengsort/indexmodule with the following changes:--bisulfitemodePR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda