Migrate to topic channels for versions #431
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Updated CHANGELOG for version 3.2.0 with changes and dependency updates.
jonasscheid
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Jan 9, 2026
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@jonasscheid I've opened a new pull request, #433, to work on those changes. Once the pull request is ready, I'll request review from you. |
Co-authored-by: jonasscheid <[email protected]>
Remove cache buster artifacts from topic channel migration
jonasscheid
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Joon-Klaps
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Jan 9, 2026
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Not 100% certain if everything went ok with template merge.
Think you might to fix of couple stuff first before the linter will be happy.
| tuple val(meta), path("*.psmpkl") , emit: psmpkl | ||
| tuple val(meta), path("*.peakpkl"), emit: peakpkl | ||
| path "versions.yml" , emit: versions | ||
| tuple val("${task.process}"), val('easypqp'), eval("easypqp --version 2>&1 | grep -oP '(?<=easypqp, version )\\d+\\.\\d+\\.\\d+'"), emit: versions, topic: versions |
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Are you sure you want to create a topic and emit variable with the same name. I think it's the first time I see this, typically it's convert_versions.
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Same goes for all other files migrations
| script: | ||
| def prefix = task.ext.prefix ?: "${meta.id}_resolved" | ||
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| """ | ||
| IDConflictResolver \\ | ||
| -in $consensus \\ | ||
| IDConflictResolver -in $consensus \\ |
| def args = task.ext.args ?: '' | ||
| def out_names = idxmls.collect { it.baseName.replace('_fdr_filtered','')+'.trafoXML' }.join(' ') | ||
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You have them in quite a few files, double check if this is inetentional that you add an empty line with just spaces in them.
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I see you also updated a lot of nf-core modules. Think it would be best if you patched them as well in nf-core/modules repo themselves.
Did it pass linting given that all md5sums will be different for these modules
| // Raw file conversion | ||
| THERMORAWFILEPARSER(branched_ms_files.raw) | ||
| ch_versions = ch_versions.mix(THERMORAWFILEPARSER.out.versions) | ||
| // ch_versions = ch_versions.mix(THERMORAWFILEPARSER.out.versions) |
| PREPARE_SPECTRA(ch_samplesheet) | ||
| ch_versions = ch_versions.mix(PREPARE_SPECTRA.out.versions) | ||
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| // Decoy Database creation |
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woops duplicate line, also i see some commented out lines that can be removed
Suggested change
| // Decoy Database creation |
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Merge after #429
Nf-core module topic channel merge should be the next step. I did migrate to topic channels in pipeline nf-core modules for consistency reasons.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).