nf-core/methylseq

View on GitHub

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair

Stars: 198
Forks: 181
Open beginner issues: 0
Indexed issues: 26
Avg merge: 6d 17h
Merged PRs (30d): 1

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: No beginner labels indexed

Beginner friendly Everything

Open All

26 open issues indexed

Add 5-bases Illumina kit support Open

enhancement

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

nf-core/methylseq#619 · Opened Jul 24, 2026
Adopt combined-index Bismark alignment modes / rethink the --multicore default (Bismark 3.1.0) Open

enhancement

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

nf-core/methylseq#615 · 3 comments · Opened Jul 15, 2026
Calling variants with rastair in the TAPS branch Open

enhancement

nf-core/methylseq#611 · 3 comments · 1 assignee · Opened Jul 11, 2026
bwameth symlink bug Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/methylseq#608 · 6 comments · Opened May 6, 2026
--igenomes_base could not validate file format Open

bug

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

nf-core/methylseq#605 · Opened Apr 21, 2026
Add sample methylation summary for the Methyldackel workflow Open

enhancement

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

nf-core/methylseq#601 · Opened Mar 23, 2026
speed issues Open

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

nf-core/methylseq#600 · Opened Mar 20, 2026
Bismark alignment failure (0% mapping) caused by Bowtie2 2.5.5 regression with EM-seq paired-end parameters Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 58/100

nf-core/methylseq#599 · Opened Mar 16, 2026
bwa-mem aligner not using GPU Open

enhancement

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

nf-core/methylseq#597 · Opened Mar 3, 2026
`PICARD_COLLECTHSMETRICS` process is skipped due to empty input channel Open

bug

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

nf-core/methylseq#596 · Opened Feb 26, 2026
Option --unmapped does not run Bismark with --unmapped argument Open

bug

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

nf-core/methylseq#595 · Opened Jan 20, 2026
Resume function is re-doing alignments instead of resuming at methylation calls Open

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

nf-core/methylseq#594 · 2 comments · Opened Jan 19, 2026
Inconsistent explanations about "--zymo" in methylseq v4.2.0 documentation Open

bug

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

nf-core/methylseq#591 · 1 comment · 1 reaction · Opened Dec 18, 2025
Workflow exits after TrimGalore with “successful” status but no alignments produced Open

bug

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

nf-core/methylseq#589 · 9 comments · Opened Dec 9, 2025
conflicting advice in usage document Open

bug

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

nf-core/methylseq#588 · 1 comment · Opened Dec 9, 2025
[bug] - samplesheet schema for genome field too strict Open

Difficulty 1/5 Under an hour Newbie friendliness 68/100

nf-core/methylseq#587 · Opened Dec 9, 2025
Support multiple bed files for targeted sequencing analysis Open

enhancement

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

nf-core/methylseq#573 · Opened Oct 27, 2025
Running in `-stub` mode fails for BISMARK_SUMMARY Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

nf-core/methylseq#527 · 1 comment · Opened May 9, 2025
Bismark soft clip --local_alignment True keeps L,value,value Open

bug

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

nf-core/methylseq#472 · 1 comment · Opened Nov 27, 2024
Add minimap2 as aligner option for Bismark Open

enhancement

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

nf-core/methylseq#455 · Opened Nov 12, 2024
Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency Open

enhancement

nf-core/methylseq#394 · 7 comments · 2 reactions · 1 assignee · Opened Apr 1, 2024
Support for NuGEN Ovation RRBS Open

stale

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

nf-core/methylseq#376 · 2 comments · Opened Jan 19, 2024
Add `rastair` Open

enhancement

nf-core/methylseq#374 · 1 comment · 1 assignee · Opened Jan 16, 2024
Mapping samples to multiple reference fasta Open

dsl2 enhancement

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

nf-core/methylseq#181 · 15 comments · 1 reaction · Opened Nov 30, 2020
Complexity curve Open

question stale

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

nf-core/methylseq#96 · 5 comments · Opened May 21, 2019
Add SNP calling Open

enhancement

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

nf-core/methylseq#65 · 6 comments · Opened Jan 30, 2019

nf-core/methylseq

Get new issues in your inbox