nf-core/pathogensurveillance

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Surveillance of pathogens using population genomics and sequencing

Stars: 61
Forks: 8
Open beginner issues: 0
Indexed issues: 43
Avg merge: 2d 6h
Merged PRs (30d): 1

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 27, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue

Beginner friendly Everything

Open All

43 open issues indexed

Handle reads with no quality scores Open

nf-core/pathogensurveillance#203 · 1 assignee · Opened Jun 2, 2026
Handle SRA accessions that dont have data assocaited with them Open

nf-core/pathogensurveillance#201 · 1 assignee · Opened Apr 30, 2026
Modifications to the dashboard report layout Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/pathogensurveillance#199 · Opened Apr 8, 2026
Add warning when the user defined references that are not used. Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/pathogensurveillance#198 · Opened Feb 27, 2026
Add DOI to nextflow.config Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 65/100

nf-core/pathogensurveillance#196 · Opened Feb 16, 2026
No need to have the nft-utils-0.0.3.jar file Open

nf-core/pathogensurveillance#182 · 1 assignee · Opened Sep 4, 2025
Investigate Ariba for detecting genes from raw reads Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/pathogensurveillance#181 · Opened Aug 19, 2025
Try using `gtExtras` for tables in report Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/pathogensurveillance#179 · Opened Jul 9, 2025
Consider incorperating geneHapR visualizations Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/pathogensurveillance#173 · 1 comment · Opened May 20, 2025
Heatmap grid line color with many samples Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/pathogensurveillance#170 · Opened May 15, 2025
changes to metro chart Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/pathogensurveillance#169 · Opened May 13, 2025
Align whole long reads instead of chopping them up, perhaps using minimap2 Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/pathogensurveillance#164 · Opened Apr 22, 2025
Pipeline errors on graphtyper, can't find a bam file. Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/pathogensurveillance#162 · 1 comment · Opened Apr 22, 2025
Save messages.tsv and versions.yml somewhere in the main input besides the report input Open

nf-core/pathogensurveillance#161 · 1 assignee · Opened Apr 16, 2025
Update BUSCO_DOWNLOAD to add lineage to output folder name Open

nf-core/pathogensurveillance#160 · 1 assignee · Opened Apr 4, 2025
Add alternative to `report_group_ids` column that takes column names to base groups on Open

good first issue

nf-core/pathogensurveillance#158 · 1 assignee · Opened Apr 2, 2025
Consider combining shared parts of the BUSCO and core gene phylogeny workflows into a single workflow Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/pathogensurveillance#152 · Opened Feb 17, 2025
Input data format rework Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/pathogensurveillance#150 · Opened Feb 13, 2025
Track original row number in sample data sheet for reporting errors to the user Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/pathogensurveillance#146 · Opened Feb 9, 2025
Add option to error and stop execution instead of issuing warnings when checking sample sheet Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/pathogensurveillance#145 · Opened Feb 8, 2025
With dorado correct producing fasta read files, could the pipeline take fasta files as input? Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/pathogensurveillance#144 · Opened Feb 7, 2025
Set enable = FALSE instead of erroring when reasonable in `check_samplesheet.R` Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

nf-core/pathogensurveillance#143 · Opened Feb 7, 2025
Handle biosamples that are assocaited with assemblies instead of reads Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/pathogensurveillance#142 · Opened Feb 6, 2025
Support 454 or see how to handle them Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/pathogensurveillance#138 · 1 comment · Opened Jan 30, 2025
Use NCBI metadata for defualt coloring of plots Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/pathogensurveillance#125 · Opened Dec 3, 2024
IQ-tree SNP error Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

nf-core/pathogensurveillance#124 · 2 comments · Opened Dec 3, 2024
Error if users give percentages to arguments that require proportions Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/pathogensurveillance#123 · Opened Dec 2, 2024
ASSIGN_CONTEXT_REFERENCES error Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/pathogensurveillance#121 · 1 comment · Opened Nov 21, 2024
Consider changing MSN threshold to number of SNPs Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/pathogensurveillance#120 · Opened Nov 19, 2024
Name dropdown entires for MSN by reference taxon name Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/pathogensurveillance#117 · Opened Nov 18, 2024
Add option to specify number of replicates when downloading references Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

nf-core/pathogensurveillance#115 · Opened Nov 18, 2024
accept assemblies as well as reads Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/pathogensurveillance#114 · Opened Nov 8, 2024
Add module to check quality of Spades assembly Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/pathogensurveillance#105 · Opened Oct 28, 2024
Change assign_context_references.R to give more informative error message Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

nf-core/pathogensurveillance#104 · Opened Oct 28, 2024
Failed rendering report Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/pathogensurveillance#103 · 2 comments · Opened Oct 23, 2024
Add maximum file size parameter to filtered downloaded assemblies and reads Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/pathogensurveillance#91 · Opened Aug 14, 2024
BUSCO graphs for assembled genomes Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/pathogensurveillance#77 · 2 comments · Opened Jun 3, 2024
Graphtyper flag may need to be added if working with Nanopore data otherwise empty merged vcf file Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/pathogensurveillance#70 · 4 comments · 1 reaction · Opened May 2, 2024
README enhancements Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/pathogensurveillance#64 · Opened Apr 22, 2024
If there are no variants print a warning message in messages.tsv Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/pathogensurveillance#52 · Opened Apr 10, 2024
Including number of genes and SNPs used to build trees Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/pathogensurveillance#50 · 1 comment · Opened Mar 27, 2024
Consider using GBIF/refseq occurrences to make a map of species occurrence for species found Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/pathogensurveillance#39 · Opened Nov 14, 2023
Figure out good default thresholds for filtering sendsketch results Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/pathogensurveillance#11 · Opened Aug 9, 2023

nf-core/pathogensurveillance

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