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@nf-core-bot fix linting |
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| tuple val(meta), path("${meta.id}.tsv"), emit: classification_file | ||
| tuple val(meta), path("${meta.id}.classified*"), optional: true, emit: fastq_classified | ||
| tuple val(meta), path("${meta.id}.unclassified*"), optional: true, emit: fastq_unclassified | ||
| tuple val("${task.process}"), val('centrifuger'), eval("centrifuger -v 2>&1 | head -n 1 | cut -d ' ' -f 2 | sed 's/^v//'"),emit: versions_centrifuger, topic: versions |
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| tuple val("${task.process}"), val('centrifuger'), eval("centrifuger -v 2>&1 | head -n 1 | cut -d ' ' -f 2 | sed 's/^v//'"),emit: versions_centrifuger, topic: versions | |
| tuple val("${task.process}"), val('centrifuger'), eval("centrifuger -v 2>&1 | sed 's/Centrifuger v//'"),emit: versions_centrifuger, topic: versions |
no need to be so fancy 🙂
famosab
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Apr 21, 2026
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Thank you for your contribution to nf-core! We really appreciate it. I added a few comments to your PR.
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| { assert snapshot( | ||
| file(process.out.classification_file[0][1]).name, | ||
| file(process.out.fastq_classified[0][1]).name, | ||
| file(process.out.fastq_unclassified[0][1]).name, | ||
| process.out.findAll { key, val -> key.startsWith('versions') } | ||
| ).match() } |
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You can use
{ assert snapshot(sanitizeOutput(process.out)).match() }
for the stub assertion. It should not be necessary to do any other assertions in the stub test.
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| file(process.out.classification_file[0][1]).name, | ||
| file(process.out.fastq_classified[0][1]).name, | ||
| file(process.out.fastq_unclassified[0][1]).name, | ||
| process.out.findAll { key, val -> key.startsWith('versions') } |
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Are all of these files instable in md5sum?
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classification_file has a stable MD5, but the classified/unclassifeid are empty due to the tiny test database that was made - so linter rejects it.
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then lets get the md5sum of classification_file and leave the names for the other :)
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Thanks for the comments and suggestions |
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Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
famosab
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Apr 22, 2026
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Last stretch, once these are addressed you're good to go!
| } | ||
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| } | ||
| test("sarscov2 - fastq_single_end_stub") { |
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| test("sarscov2 - fastq_single_end_stub") { | |
| test("sarscov2 - fastq - single_end - stub") { |
| ) | ||
| } | ||
| } | ||
| test("sarscov2 - fastq_paired_end") { |
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| test("sarscov2 - fastq_paired_end") { | |
| test("sarscov2 - fastq - paired_end") { |
| } | ||
| } | ||
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| test("sarscov2 - fastq_single_end") { |
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Suggested change
| test("sarscov2 - fastq_single_end") { | |
| test("sarscov2 - fastq - single_end") { |
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To follow our typical convention
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/centrifuger:1.1.0--hf426362_0': | ||
| 'biocontainers/centrifuger:1.1.0--hf426362_0' }" |
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This was changed like 2 days ago
Suggested change
| 'biocontainers/centrifuger:1.1.0--hf426362_0' }" | |
| 'quay.io/biocontainers/centrifuger:1.1.0--hf426362_0' }" |
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| input: | ||
| tuple val(meta), path(reads) | ||
| path db |
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I would argue the db could also have a meta (in this case meta2 - we use meta with databases in taxprofiler)
Suggested change
| path db | |
| tuple val(meta2), path(db) |
If you go with it, make sure to update the tests
| ${umi_arg} \\ | ||
| -t ${task.cpus} \\ | ||
| ${args} > ${prefix}.tsv | ||
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| #main output | ||
| touch ${prefix}.tsv | ||
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| #Optional outputs |
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Suggested change
| #Optional outputs | |
| ## Optional outputs |
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| echo ${args} | ||
| #main output |
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Suggested change
| #main output | |
| ## main output |
| - edam: http://edamontology.org/format_1930 #FASTQ | ||
| - db: | ||
| type: directory | ||
| description: Path to directory containing Centrifuger database files. |
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| description: Path to directory containing Centrifuger database files. | |
| description: Path to directory containing Centrifuger database files (that end in `.cfr`). |
| - ${meta.id}.tsv: | ||
| type: file | ||
| description: | | ||
| File contαining classification results |
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| File contαining classification results | |
| File containing classification results |
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PR checklist
Closes #XXX
topic: versionslabelnf-core modules test centrifuger/centrifuger --profile dockernf-core modules test centrifuger/centrifuger --profile singularitynf-core modules test centrifuger/centrifuger --profile condaDescription
Classificion model for Centrifguer modules
Module details
.cfrfiles).cfrfiles) may need to be rebuilt on a native x86 machine .