nf-core/pacvar

Longread PacBio sequencing processing for WGS and PureTarget

Beginner friendly Everything

Open All

10 open issues indexed

hiphase/PREFIX.snv.phased.vcf should have the .gz suffix & lacks a .tbi Open

bug

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

nf-core/pacvar#69 · Opened Aug 1, 2026
Issue with pbmm2 and Vega data Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/pacvar#68 · Opened Jul 30, 2026
Allow Ensembl VEP to take plugins and custom files Open

enhancement

nf-core/pacvar#60 · 1 assignee · Opened Jun 19, 2026
Update the `HiPhase` module Open

enhancement

nf-core/pacvar#59 · 1 assignee · Opened Jun 19, 2026
swapping the remaining modules to use topics Open

enhancement

nf-core/pacvar#58 · 1 assignee · Opened Jun 19, 2026
PBSV_CALL inserts NUL bytes (^@) in the middle of a record? Open

bug help wanted

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

nf-core/pacvar#47 · 1 comment · Opened Apr 6, 2026
Replace pipeline parameter `skip_snp` to `skip_snv` Open

enhancement

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

nf-core/pacvar#45 · Opened Mar 16, 2026
GATK needs a sequence dictionary to run Open

enhancement

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

nf-core/pacvar#27 · 3 comments · Opened Mar 1, 2025
ERROR nextflow.cli.Launcher Open

Difficulty 4/5 3-5 days Newbie friendliness 18/100

nf-core/pacvar#18 · 3 comments · Opened Feb 13, 2025
Expand on possible ref genome suffixes Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 32/100

nf-core/pacvar#16 · Opened Feb 12, 2025

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