nf-core/viralintegration

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Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

Stars: 19
Forks: 11
Open beginner issues: 0
Indexed issues: 22

Dominant language: Python
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

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22 open issues indexed

Running Nextflow run on an ARM64 Architecture Server Open

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

nf-core/viralintegration#86 · Opened Apr 9, 2026
viralintegration on bacteria Open

enhancement

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

nf-core/viralintegration#85 · Opened Mar 18, 2026
nf-core/viralintegration suitable for TES data? Open

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

nf-core/viralintegration#83 · Opened May 21, 2025
JSON schema: Viralintegration Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/viralintegration#82 · Opened Mar 25, 2025
Error in STAR_ALIGN: Segmentation fault with STAR v2.7.9a Open

bug

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

nf-core/viralintegration#81 · Opened Nov 13, 2024
refine_VIF_output.R fails when *.vif.evidence_counts.tsv is empty Open

bug

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

nf-core/viralintegration#80 · 3 comments · Opened Jul 25, 2024
Mulitmapping reads dropped resulting in empty output files using GRCh37 Open

bug

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

nf-core/viralintegration#77 · Opened Apr 2, 2024
The pipeline failed on the test_full profile option (segmentation fault, exit code 139) Open

bug

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

nf-core/viralintegration#76 · 1 comment · Opened Mar 7, 2024
URGENT: pin nf-validation version Open

bug

nf-core/viralintegration#74 · 1 comment · 1 assignee · Opened Feb 22, 2024
chimeric_contig_evidence_analyzer.py removed all reads Open

bug

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

nf-core/viralintegration#70 · 1 comment · Opened Jan 15, 2024
Aligner choice in viralintegration pipeline Open

bug

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

nf-core/viralintegration#66 · Opened Oct 18, 2023
Add support for single end reads Open

enhancement

nf-core/viralintegration#64 · 1 assignee · Opened Aug 22, 2023
Add subworkflows Open

enhancement

nf-core/viralintegration#58 · 1 assignee · Opened Mar 27, 2023
Add viRNAtrap to pipeline Open

enhancement

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

nf-core/viralintegration#56 · Opened Feb 13, 2023
Processes to turn into a subworkflow Open

nf-core/viralintegration#53 · 1 assignee · Opened Jan 24, 2023
v1.0.0 Release Criteria Open

enhancement

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

nf-core/viralintegration#51 · Opened Jan 11, 2023
Update documentation and add example analysis Open

enhancement

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

nf-core/viralintegration#48 · Opened Dec 26, 2022
Look into failing md5sums on CI Open

bug

nf-core/viralintegration#47 · 1 assignee · Opened Dec 23, 2022
Update test data for nf-test/summary_report Open

enhancement

nf-core/viralintegration#37 · 2 comments · 1 assignee · Opened Nov 16, 2022
Replace bamsifter with deepTools bamCoverage Open

enhancement

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

nf-core/viralintegration#25 · Opened Jul 14, 2022
Use CTAT singularity image Open

enhancement

nf-core/viralintegration#21 · 1 comment · 1 assignee · Opened Jun 29, 2022
Add MetaPhlAn 3.0 module Open

enhancement

nf-core/viralintegration#2 · 1 comment · 1 assignee · Opened Apr 22, 2022

nf-core/viralintegration

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