nf-core/phageannotator

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Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.

Stars: 19
Forks: 8
Open beginner issues: 0
Indexed issues: 51

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 28, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

51 open issues indexed

No fasta input implemented? Open

bug

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

nf-core/phageannotator#129 · Opened Jun 12, 2025
iPHOP downloads the wrong database for its current version Open

bug

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

nf-core/phageannotator#127 · Opened May 1, 2025
Running geNomad and COBRA fails because of altered FASTA sequence name Open

bug

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

nf-core/phageannotator#125 · Opened Apr 25, 2025
COBRA options schema are listed as strings when they should be ints Open

bug

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

nf-core/phageannotator#123 · 1 comment · Opened Apr 24, 2025
Add prophage tracer to predict prophage activity Open

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

nf-core/phageannotator#113 · Opened Apr 18, 2024
Replace mash screen with sylph Open

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

nf-core/phageannotator#112 · Opened Apr 18, 2024
Replace BLAST with skani for ani clustering Open

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

nf-core/phageannotator#111 · Opened Apr 18, 2024
Add clustering with Inphared to assign ICTV taxonomy Open

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

nf-core/phageannotator#105 · Opened Mar 20, 2024
Add viralFlye to nf-core phageannotator Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/phageannotator#104 · Opened Mar 18, 2024
Prepare phageannotator for first release Open

Difficulty 5/5 Over a week Newbie friendliness 1/100

nf-core/phageannotator#103 · Opened Mar 16, 2024
Update nf-core/phageannotator nf-test structure to match fetchngs Open

nf-core/phageannotator#94 · 1 assignee · Opened Feb 19, 2024
Update nf-tests so full modules are only run in module tests Open

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

nf-core/phageannotator#93 · 1 comment · Opened Feb 15, 2024
Add ability to start nf-core/phageannotator with fastq only, fasta only, or a combination of both Open

enhancement

nf-core/phageannotator#90 · 1 assignee · Opened Feb 6, 2024
Add phanta to nf-core/phageannotator Open

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

nf-core/phageannotator#87 · Opened Jan 22, 2024
Add vRhyme to nf-core/phageannotator Open

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

nf-core/phageannotator#85 · Opened Jan 18, 2024
Add genus/family-level clustering to nf-core/phageannotator Open

Difficulty 5/5 Over a week Newbie friendliness 10/100

nf-core/phageannotator#84 · Opened Jan 11, 2024
Update nf-core/phageannotator local modules/subworkflows Open

nf-core/phageannotator#83 · 1 assignee · Opened Jan 2, 2024
Auto generate nf-core/differentialabundance samplesheet using nf-core/phageannotator Open

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

nf-core/phageannotator#76 · Opened Dec 15, 2023
Auto generate nf-core/funscan samplesheet using nf-core/phageannotator Open

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

nf-core/phageannotator#75 · Opened Dec 15, 2023
Auto generate nf-core/mag samplesheet using nf-core/taxprofiler Open

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

nf-core/phageannotator#74 · Opened Dec 15, 2023
Auto generate nf-core/mag samplesheet using nf-core/fetchngs Open

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

nf-core/phageannotator#73 · Opened Dec 15, 2023
Add phanta to nf-core/taxprofiler Open

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

nf-core/phageannotator#72 · Opened Dec 15, 2023
Add phanta to nf-core/modules Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/phageannotator#71 · Opened Dec 15, 2023
Add phanta to nf-core/taxprofiler Open

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

nf-core/phageannotator#70 · Opened Dec 15, 2023
Add VirSorter2 to nf-core/phageannotator Open

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

nf-core/phageannotator#69 · Opened Dec 15, 2023
Add VirSorter2 to nf-core/modules Open

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

nf-core/phageannotator#68 · Opened Dec 15, 2023
Add other phage identification options to nf-core/phageannotator Open

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

nf-core/phageannotator#67 · Opened Dec 15, 2023
Add ViromeQC to nf-core/phageannotator Open

Difficulty 4/5 3-5 days Newbie friendliness 10/100

nf-core/phageannotator#66 · Opened Dec 15, 2023
Add ViromeQC to nf-core/modules Open

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

nf-core/phageannotator#65 · Opened Dec 15, 2023
Update ViromeQC on BIoconda Open

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

nf-core/phageannotator#64 · Opened Dec 15, 2023
Add mash/dist to nf-core/phageannotator Open

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

nf-core/phageannotator#62 · Opened Dec 15, 2023
Add mash/sketch for external database to nf-core/phageannotator Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/phageannotator#61 · Opened Dec 15, 2023
Add mash reference database comparison to nf-core/phageannotator Open

Difficulty 5/5 Over a week Newbie friendliness 32/100

nf-core/phageannotator#60 · Opened Dec 15, 2023
Add propAgatE to nf-core/phageannotator Open

Difficulty 4/5 3-5 days Newbie friendliness 10/100

nf-core/phageannotator#59 · Opened Dec 15, 2023
Add propAgatE to nf-core/modules Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/phageannotator#58 · Opened Dec 15, 2023
Add propAgate to Bioconda Open

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

nf-core/phageannotator#57 · Opened Dec 15, 2023
Add vCONTACT3 to nf-core/phageannotator Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/phageannotator#56 · Opened Dec 15, 2023
Add vCONTACT3 to nf-core/modules Open

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

nf-core/phageannotator#55 · Opened Dec 15, 2023
Add vcontact3 to nf-core/phageannotator Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/phageannotator#54 · Opened Dec 15, 2023
Add UHGV Classify to nf-core/phageannotator Open

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

nf-core/phageannotator#53 · Opened Dec 15, 2023
Add UHGV Classify to nf-core/modules Open

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

nf-core/phageannotator#52 · Opened Dec 15, 2023
Add UHGV Classify to Bioconda Open

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

nf-core/phageannotator#51 · Opened Dec 15, 2023
Add COBRA to bioconda Open

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

nf-core/phageannotator#48 · Opened Dec 15, 2023
Add nf-core/phageannotator's local modules/subworkflows to nf-core Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/phageannotator#39 · Opened Nov 30, 2023
Add UHGV classify to nf-core/phageannotator Open

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

nf-core/phageannotator#37 · Opened Nov 30, 2023
Add auto-generate samplesheet to nf-core/mag Open

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

nf-core/phageannotator#34 · Opened Nov 30, 2023
Add propagate to nf-core/phageannotator to identify active prophage Open

enhancement

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

nf-core/phageannotator#19 · Opened Jul 19, 2023
Add anicalc and anicluster taxonomy modules to workflow Open

enhancement

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

nf-core/phageannotator#18 · Opened Jul 19, 2023
Add blast taxonomy modules to workflow Open

enhancement

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

nf-core/phageannotator#17 · Opened Jul 19, 2023
Add mash taxonomy modules to workflow Open

enhancement

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

nf-core/phageannotator#16 · Opened Jul 19, 2023

nf-core/phageannotator

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