nf-core/bacass

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Simple bacterial assembly and annotation pipeline

Stars: 93
Forks: 74
Open beginner issues: 0
Indexed issues: 23
Avg merge: 1d 22h
Merged PRs (30d): 2

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 help wanted

Beginner friendly Everything

Open All

23 open issues indexed

Update bacass's metro maps before 2.7.0 relese Open

enhancement

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

nf-core/bacass#322 · Opened Jul 30, 2026
Rename branch name `master` to `main` Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

nf-core/bacass#321 · Opened Jul 29, 2026
Flye duplicated reads error with autocycler (v2.6.0) Open

bug

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

nf-core/bacass#312 · 2 comments · Opened Jul 1, 2026
KmerFinder database FTP no longer available - tool renamed to SpeciesFinder Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 65/100

nf-core/bacass#296 · 3 comments · Opened Apr 16, 2026
BadZipFile Error in download_reference.py - NCBI API returns non-ZIP data with HTTP 200 Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 58/100

nf-core/bacass#290 · Opened Mar 30, 2026
Add dbCAN Open

enhancement

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

nf-core/bacass#280 · Opened Mar 11, 2026
Add genomad module Open

enhancement

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

nf-core/bacass#278 · Opened Mar 11, 2026
Add traitar module Open

enhancement

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

nf-core/bacass#277 · Opened Mar 11, 2026
Add GTDB-Tk for taxonomic info Open

enhancement

nf-core/bacass#274 · 1 assignee · Opened Mar 11, 2026
Make "--assembly_type" optional (change default to 'auto') Open

enhancement question

nf-core/bacass#271 · 7 comments · 1 assignee · Opened Mar 2, 2026
JSON schema: Bacass Open

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

nf-core/bacass#217 · Opened Mar 25, 2025
Add nº round of polishing (racon+minimap) ONT Open

enhancement

nf-core/bacass#214 · 1 assignee · Opened Mar 24, 2025
Add genome rotation step to start chromosomes at dnaA Open

enhancement

nf-core/bacass#212 · 1 comment · 1 assignee · Opened Mar 23, 2025
Add dnapler module (genome rotation to dnaA) Open

enhancement

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

nf-core/bacass#211 · Opened Mar 23, 2025
Add gfastats module (structural assembly statistics) Open

enhancement

nf-core/bacass#209 · 1 assignee · Opened Mar 23, 2025
Add ciclator module (structural reorientation) Open

enhancement

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

nf-core/bacass#204 · Opened Mar 23, 2025
Add when condition and stub section in local modules Open

enhancement

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

nf-core/bacass#200 · Opened Mar 21, 2025
Addd a Nextflow configuration test profile to validate the KmerFinder step Open

enhancement

nf-core/bacass#197 · 1 assignee · Opened Mar 14, 2025
Error in racon step when running miniasm assembler Open

bug

nf-core/bacass#194 · 1 comment · 1 assignee · Opened Feb 24, 2025
MultiQC Version 1.21 Parsing Issue Open

enhancement

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

nf-core/bacass#142 · Opened Jun 13, 2024
Single end Illumina processing? Open

enhancement

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

nf-core/bacass#82 · 1 comment · Opened Mar 8, 2023
Add homopolish for nanopore-only assembly Open

enhancement good first issue

nf-core/bacass#66 · 2 comments · 1 assignee · Opened Sep 20, 2021
List of ideas to improve assemblies Open

enhancement help wanted question

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

nf-core/bacass#57 · 9 comments · Opened Aug 19, 2021

nf-core/bacass

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