nf-core/pathogenepidemiology

[UNDER DEVELOPMENT] A profile-based pipeline for genomic epidemiological analysis of predefined pathogens.

Stars: 3
Forks: 2
Open beginner issues: 0
Indexed issues: 9
Avg merge: 2d 23h
Merged PRs (30d): 6

Dominant language: Nextflow
License: MIT
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

9 open issues indexed

BBDUK step takes forever to test - solutions? Open

question

nf-core/pathogenepidemiology#13 · 3 comments · 1 assignee · Opened Aug 3, 2026
Decide details of population-aware layer Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/pathogenepidemiology#10 · Opened Jul 29, 2026
Write GATK step according to Niaré et al. protocol Open

nf-core/pathogenepidemiology#8 · 2 assignees · Opened Jul 28, 2026
Create short read analysis track Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/pathogenepidemiology#7 · 1 comment · Opened Jul 28, 2026
Handle reference downloads Open

nf-core/pathogenepidemiology#6 · 1 comment · 1 assignee · Opened Jul 28, 2026
Integrate code from `workflows/original_local.nf` into `workflows/pathogenepidemiology.nf` Open

nf-core/pathogenepidemiology#5 · 1 assignee · Opened Jul 28, 2026
Decide on Long Read variant caller that supports polyploidy (fit for MOI analysis) Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

nf-core/pathogenepidemiology#4 · Opened Jul 28, 2026
Update metromap Open

nf-core/pathogenepidemiology#2 · 1 assignee · Opened Jul 28, 2026
Support for samples with long and short read types Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/pathogenepidemiology#1 · 2 comments · Opened Jul 28, 2026

A short digest of beginner-friendly GitHub issues.