Prevent execution of gtdbtk/summary when no bins pass QC#1021
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gtdbtk/summary when no bins passed QCgtdbtk/summary when no bins pass QC
jfy133
approved these changes
Apr 9, 2026
| ch_bin_qc_summary | ||
| .count() | ||
| .filter { count -> count == 0 } | ||
| .subscribe { _count -> |
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What does the subscribe do here 🤔 I never understood that operator...
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subscribe() executes a function on each output of a channel, without generating an ouput (contrary to map() that returns something)
dialvarezs
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Apr 9, 2026
Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com>
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This removes the
.ifEmpty()ofGTDBTK_CLASSIFYWF.out.summaryto prevent runningGTDBTK_SUMMARYwhen no summaries are available.It also adds a warning when no bins passed QC thresholds.
Closes #981.
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).