Important! Template update for nf-core/tools v4.0.2#1030
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nf-core-bot
requested review from
d4straub,
dialvarezs,
jfy133,
muabnezor and
prototaxites
as code owners
|
prototaxites
reviewed
May 4, 2026
| "multiqc/multiqc_data/fastqc_sequence_counts_plot.yaml", | ||
| "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.yaml", | ||
| "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.yaml", | ||
| "multiqc/multiqc_data/gtdbtk-first-table.yaml", |
Contributor
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Is there a reason we've lost a bunch of multiQC files?
Member
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This comes from the update of the MultiQC module, so no idea really.
prototaxites
reviewed
May 4, 2026
Comment on lines
-631
to
-655
| if (!params.skip_quast) { | ||
| ch_multiqc_files = ch_multiqc_files.mix(QUAST.out.report.collect().ifEmpty([])) | ||
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| if (!params.skip_binning) { | ||
| ch_multiqc_files = ch_multiqc_files.mix(QUAST_BINS.out.dir.collect().ifEmpty([])) | ||
| } | ||
| } | ||
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| if (!params.skip_binning || params.ancient_dna) { | ||
| ch_multiqc_files = ch_multiqc_files.mix(BINNING_PREPARATION.out.multiqc_files.collect().ifEmpty([])) | ||
| } | ||
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| if (!params.skip_binning) { | ||
| if (!params.skip_prokka) { | ||
| ch_multiqc_files = ch_multiqc_files.mix(PROKKA.out.txt.collect { _meta, report -> report }.ifEmpty([])) | ||
| } | ||
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| if (!params.skip_binqc) { | ||
| ch_multiqc_files = ch_multiqc_files.mix(BIN_QC.out.multiqc_files.collect().ifEmpty([])) | ||
| } | ||
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| if (!params.skip_gtdbtk) { | ||
| ch_multiqc_files = ch_multiqc_files.mix(GTDBTK.out.multiqc_files.collect().ifEmpty([])) | ||
| } | ||
| } |
Contributor
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It looks like a bunch of stuff is no longer being fed to MQC?
Member
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You're right! My bad, fixing it now.
prototaxites
approved these changes
May 4, 2026
prototaxites
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Contributor
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LGTM now! Feel free to merge, but might be good to double-check the output MQC report first if you haven't'
Member
|
I checked the MultiQC reports and they look fine. Thank you @prototaxites! |
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Version
4.0.2of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/blog/2026/tools-4_0_0Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-4.0.2branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.For instructions on how to merge this PR, please see the template sync documentation.
For more information about this release of nf-core/tools, please see the
v4.0.2release page.Note
Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. Older template PRs will be automatically closed once a newer template PR has been merged.