Add stub block and migrate plasmidid to topic channels#11438
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@nf-core-bot fix linting |
LouisLeNezet
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LouisLeNezet
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Hi,
Just a few changes needed before approval
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(sanitizeOutput(process.out, unstableKeys:["images", "logs", "data", "database", "kmer"])).match() } |
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In the stub test all the files should be stable.
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) | ||
| ] | ||
| input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
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Please remove the empty new line as well as // meta map. This is no more needed.
| tuple val(meta), path("${prefix}/fasta_files/") , emit: fasta_files | ||
| tuple val(meta), path("${prefix}/kmer/") , emit: kmer | ||
| path "versions.yml" , emit: versions | ||
| tuple val("${task.process}"), val('plasmidid'), eval('echo "$(plasmidID --version 2>&1)" | sed "s/^plasmidID //"'), topic: versions, emit: versions_plasmidid |
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This can be simplified as
| tuple val("${task.process}"), val('plasmidid'), eval('echo "$(plasmidID --version 2>&1)" | sed "s/^plasmidID //"'), topic: versions, emit: versions_plasmidid | |
| tuple val("${task.process}"), val('plasmidid'), eval("plasmidID --version 2>&1| sed 's/^plasmidID //'"), topic: versions, emit: versions_plasmidid |
| def args = task.ext.args ?: '' | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| mkdir -p ${prefix}/images ${prefix}/logs ${prefix}/data ${prefix}/database ${prefix}/fasta_files ${prefix}/kmer |
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Could you add some files in the empty folders that correspond to what is present in the real test ?
| pattern: "*.{tab}" | ||
| ontologies: | ||
| - edam: http://edamontology.org/format_3475 # TSV | ||
| - edam: http://edamontology.org/format_3475 |
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Please keep the comment
| - edam: http://edamontology.org/format_3475 | |
| - edam: http://edamontology.org/format_3475 # TSV |
- Replace versions.yml with eval() topic: versions emission - Simplify version command per reviewer suggestion - Add stub block with representative files in all output directories - Remove unstableKeys from stub test (stubs are deterministic) - Remove // meta map comments and blank lines from tests - Restore EDAM # TSV comment on tab output - Regenerate meta.yml, remove legacy versions output
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Thanks for the review @LouisLeNezet! All feedback addressed: ✅ Removed Verification: Note on Conda CI failure: This is a pre-existing upstream issue unrelated to this PR (the |
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Changes
versions.ymlheredoc totopic: versionstuple patternstub:block creating all 8 output directories and touch filesmeta.ymlto align withmain.nfVerification
nf-core modules lint plasmidid: 53/53 passed, 0 failuresnf-test(Docker): 2/2 passed, snapshots stable across consecutive runsPart of #4570