Update sourmash sketch to remove hardcoded optional argument - #12999
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SPPearce merged 36 commits intoSep 20, 2026
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@nf-core-bot fix linting |
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Ugh failing tests... I bet because of row ordering 🙄 |
…m:jfy133/nf-core-modules into sourmash-sketch-remove-optional-parameter
SPPearce
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Sep 20, 2026
Midnighter
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Sep 20, 2026
| Specify whether to merge the signatures of all input files into a single signature file. | ||
| Used e.g. for paired-end FASTQ inputs, or when there are multiple FASTAs for a single genome (such as chromosomes or contigs). | ||
| Signature name will be set to the processes' '${prefix}'. | ||
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Sorry for being late to the party @jfy133, why this extra input rather than relying on ext.args set by a user?
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Because the original implementation used prefix as the default name (which is a reasonable assumption in this case), but prefix is not accessible via modules.conf.
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I was about to push same PR for merge and i just saw yours, i guess no need anymore :) |
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Sep 22, 2026
…#12999) * Bump das_tool versions * Roll back scaffolds2binversion as this is a legacy * Correct build container * Missing quote * Fix bug in conda scope check condition for antismash download databases * Update main.nf * Update Kaiju to also emit the downstream required nodes file * Include names file as well * Update documentation * update all Kaiju modules to topics * Remove debug thing from sourmash * Reset KMCP files * [automated] Fix code linting * Move previous implicit (but optional) argument to input channel option * Update taxannotate tests to include missing arguments in upstream module in test * [automated] Fix code linting * Updates snapshot to account for variability * Update merge test due to random selection of main file name * Relax further --------- Co-authored-by: nf-core-bot <core@nf-co.re>
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SOURMASH_SKETCH included an actually optional argument
--mergewhich was having unintended 'hidden' behaviours in some cases.This PR moves the parameter to an input boolean, and updates all tests to keep the original behaviour using the new system.