Skip to content

Issues: nf-core/pathogensurveillance

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

38 Open 52 Closed
38 Open 52 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Error when some assembly metadata tsv files are empty and don't contain accessions to download bug Something isn't working
#94 opened Sep 18, 2024 by masudermann
Unable to finish picking assemblies
#93 opened Aug 14, 2024 by buchanri
Large and complex test data set
#92 opened Aug 14, 2024 by zachary-foster
9 tasks
Add maximum file size parameter to filtered downloaded assemblies and reads
#91 opened Aug 14, 2024 by zachary-foster
Bakta database bug ("amrfinder error") bug Something isn't working
#90 opened Aug 14, 2024 by zachary-foster
1
Error rendering report when I don't have core gene phylogeny (eukaryote dataset) bug Something isn't working
#89 opened Aug 6, 2024 by masudermann
2
Fail to create conda environment for sourmash_sketch
#87 opened Jul 25, 2024 by buchanri
1
Looking for sample sheet metadata not in the provided path
#86 opened Jul 24, 2024 by buchanri
1
BBmap_Sendsketch not finding SRA
#85 opened Jul 18, 2024 by buchanri
Sample sheet error
#83 opened Jul 15, 2024 by buchanri
1
read2tree issue on mixed dataset bug Something isn't working
#82 opened Jul 15, 2024 by masudermann
Error when testing xanthomonas small dataset bug Something isn't working
#81 opened Jul 15, 2024 by buchanri
Add subsetting of variants when there are more than a user-defined maximum
#80 opened Jul 2, 2024 by zachary-foster
Make SUBSET module name its output by the sample ID
#79 opened Jun 13, 2024 by zachary-foster
Make DOWNLOAD_ASSEMBLIES store data more effeciently
#78 opened Jun 13, 2024 by zachary-foster
BUSCO graphs for assembled genomes
#77 opened Jun 3, 2024 by grunwald
1
We need to review the step where we convert Graphtyper VCF outputs files to tabular format using vcf-to-tab bug Something isn't working
#76 opened May 31, 2024 by masudermann
1
Report fails to render if I don't have POCP matrix-an issue when dealing with eukaryotic datasets bug Something isn't working
#75 opened May 31, 2024 by masudermann
Killed with a warning?
#74 opened May 29, 2024 by cahuparo
Graphtyper flag may need to be added if working with Nanopore data otherwise empty merged vcf file
#70 opened May 2, 2024 by masudermann
4
README enhancements
#64 opened Apr 22, 2024 by zachary-foster
Check if type strains are being chosen for references
#61 opened Apr 17, 2024 by zachary-foster
Variant calling uses alternate reference but retains user-defined reference id bug Something isn't working
#60 opened Apr 17, 2024 by cahuparo
Docker bwa image no longer loading for docker version 25+
#58 opened Apr 15, 2024 by logankblair
Add input column to define type of nanopore/pacbio sequencing
#55 opened Apr 12, 2024 by zachary-foster
@zachary-foster
ProTip! What’s not been updated in a month: updated:<2024-09-11.