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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 ...
richard-burhans
Hello dear EGAPx team,
Recently I ve pulled the recent 1.0.1 tag version but I ve ran into a problem with the run_proteins_by_taxid subprocess.
ERROR ~ Error executing process egapx:target_proteins_plane:target_proteins_plane:proteins_by_taxid:run ...
NickPanyushev
Summary
While using multi mode to compare 8+ divergent structures against a FoldMason (structure-based) MSA, I found four
independent bugs, three of which live in code shared with single mode. Each has ...
fsberki
./bin/fasterq-dump --split-files SRR000001 ─╯ 2026-09-28T15:45:52 fasterq-dump.3.4.1 err: name not found while resolving
query within virtual file system module - failed to resolve accession SRR000001 ...
Derektshiabuila
check-corrupt exits 0 on runs it lists as corrupt, and ends with All accessions are good! when an input could not be
opened. The first is a regression from 1b56c117 (VDB-5965, in 3.3.0). Run on master ...
Santoshkumarpuppala
Describe the bug: when update_self() can t fetch the script, it prints Failed to update ./pgap.py, ignoring then calls
sys.exit(), so pgap.py exits 0 without starting the pipeline. That includes an offline ...
Hi EGAPx developers,
I am currently using EGAPx to annotate a water lily genome (Nymphaea colorata).
For the annotation, I have provided RNA-seq data as transcript evidence and specified the corresponding ...
kingbin97
Hi again, and thanks for looking at #280. While testing the same program (fg-sra) we came across a second, unrelated
crash, in ReferenceObj_Read() in libs/align/reference.c. A PR with a proposed fix follows; ...
tfenne
Hi, and thank you for ncbi-vdb and sra-tools. We use ncbi-vdb in fg-sra, and while testing it on a range of aligned runs
we hit an intermittent segfault when reading external references. We traced it to ...
I would like to use PGAP to generate gene calls that would connect one-to-one with gene calls on NCBI s PGAP. However, I
would like to do this in bulk for many MAGs, many don t have a valid genus+species ...
osvatic
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