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export() inputs passed out of order in nf/ui.nf; filtered protein alignments published under stats/rnaseq_long/ #274
Description
EGAPx version: 1.0.1
In nf/ui.nf, the export(...) call passes four channels out of order compared with the export process declaration. Nextflow binds inputs by position, so they get staged under the wrong directories:
| Position | Declared input | Channel passed |
|---|---|---|
| 21 | rnaseq_long_align_report |
filtered_protein_alignments |
| 23 | rnlp_filter_est_align_stats |
rnaseq_long_align_report |
| 24 | minimap2_stats |
rnlp_filter_est_align_stats |
| 25 | filtered_protein_alignments |
minimap2_stats |
Effect: with short reads (e.g. examples/input_D_farinae_small.yaml), filtered_protein_alignments/ is missing from the output and align.asn is publishedunder stats/rnaseq_long/ instead. With long reads, the minimap2 stats would end up in filtered_protein_alignments/.
Fix: reorder the arguments to match the declaration. PR to follow.
Activity
murphyte commentedon Oct 1, 2026
thanks, I'm surprised this didn't show up in our testing. We'll review your PR for inclusion in our next release.
ncbi_egapx: patch 0002 README: four channels, link upstream issue/PR
Egapx 1.0.1 (#178)
boukn commentedon Oct 20, 2026
this will be in our next release