Add Autocycler postassembly subworkflow #9786
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d4straub
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d4straub
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Thanks for that great addition! Looking forward to that subworkflow!
I have a few comments though.
subworkflows/nf-core/fasta_consensus_autocycler/tests/main.nf.test
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| process RENAME { | ||
| tag "$meta.id" | ||
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| input: | ||
| tuple val(meta), path(file) | ||
| val key | ||
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| output: | ||
| tuple val(meta), path("${key}_${file}"), emit: renamed | ||
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| script: | ||
| """ | ||
| ln -s ${file} "${key}_${file}" | ||
| """ | ||
| } |
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It looks unusual to me to have a process in here. I havent seen a precedence among nf-core subworkflows. Maybe that can be solved differently?
| RENAME( | ||
| AUTOCYCLER_RESOLVE.out.resolved, | ||
| AUTOCYCLER_RESOLVE.out.resolved.map{meta, file -> "${meta.id}_${meta.cluster}"} | ||
| ) |
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Potentially that could be fixed in the AUTOCYCLER_RESOLVE module? Instead of having
https://github.com/nf-core/modules/blob/e6f6c211fed71038331afa8ed963e006f9acdbc9/modules/nf-core/autocycler/resolve/main.nf#L16C5-L16C67
it could be tuple val(meta), path("${prefix}_5_final.gfa"), emit: resolved (and name the files in the module script appropriately)?
I understand that this doesnt follow the tutorial of the tool, but wont most users of that module need to fix the output naming similar to here?
delete commented out lines and add indents
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Adds subworkflow for post assembly autocycler to make it easier to run autocycler in an nf-core pipeline. Takes a list of assemblies from different assemblers or different read subsamples of a single sample. Runs autocycler compress, cluster, trim, resolve and combine. Channel manipulation to label clusters and rename files to avoid collisions.
Closes #9785
PR checklist
topic: versions- See version_topicsnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda