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.
EGAPx version: 1.0.1
In
nf/ui.nf, theexport(...)call passes four channels out of order compared with theexportprocess declaration. Nextflow binds inputs by position, so they get staged under the wrong directories:rnaseq_long_align_reportfiltered_protein_alignmentsrnlp_filter_est_align_statsrnaseq_long_align_reportminimap2_statsrnlp_filter_est_align_statsfiltered_protein_alignmentsminimap2_statsEffect: with short reads (e.g.
examples/input_D_farinae_small.yaml),filtered_protein_alignments/is missing from the output andalign.asnis publishedunderstats/rnaseq_long/instead. With long reads, the minimap2 stats would end up infiltered_protein_alignments/.Fix: reorder the arguments to match the declaration. PR to follow.