New module - TD2 (added modules for td2.longorfs & td2.predict) #9475
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SPPearce
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SPPearce
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Please look at swapping to using a topic channel to emit the version:
https://nf-co.re/blog/2025/version_topics
| """ | ||
| TD2.LongOrfs \\ | ||
| -t ${fasta} \\ | ||
| -O ${prefix} \\ |
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Can we just make the files directly in this folder, rather than a subfolder?
| tuple val(meta), path(fasta) | ||
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| output: | ||
| tuple val(meta), path("${prefix}/longest_orfs.{cds,gff3,pep}"), emit: orfs |
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We generally make one output channel per file, rather than multiple in one, unless there is a good reason otherwise.
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| td2: \$(td2 v1.0.6) |
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This should be getting the version from the tool.
If the tool doesn't give a version, it should be set as a separate string with warnings to ensure people remember to change if they change the version.
https://github.com/search?q=repo%3Anf-core%2Fmodules+%22not+provided+by+tool+on+CLI%22
| }, | ||
| { | ||
| "TD2_PREDICT": { | ||
| "td2": null |
| "community.wave.seqera.io/library/td2:1.0.6--ea3e5ac09443b677"}" | ||
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| input: | ||
| tuple val(meta), path(fasta), path(orfs_dir, stageAs: 'orfs') |
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Hmm, so this tool requires all three files in one directory? Then I can see a reason to emit them as one channel above.
Added new modules for TD2 -
longorfsandpredictCloses #9470
versions.ymlfile.labelnf-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