Skip to content

Issues: nf-core/methylseq

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

42 Open 84 Closed
42 Open 84 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

samplesheet handling: different path + same filename gives a bug bug Something isn't working
#407 opened Jun 28, 2024 by AdrijaK
Multiple issues in the pipeline bug Something isn't working
#406 opened Jun 25, 2024 by gevro
Bwameth vs bismark
#405 opened Jun 23, 2024 by gevro
Adding --maxVariantFrac and --minOppositeDepth to MethylDackel (Bwameth option) enhancement New feature or request
#404 opened Jun 18, 2024 by LucaZanella15
Write tests for samplesheet sample merging/grouping
#402 opened May 21, 2024 by edmundmiller 2.7.0
@FelixKrueger @sateeshperi
AS-XS tag missing enhancement New feature or request
#397 opened May 1, 2024 by AndreiWCansor
bwameth pipeline skipping all bwameth steps when --fasta, --fasta_index, and --bwa_meth_index are provided. bug Something isn't working
#396 opened Apr 5, 2024 by drothen15
2
Schematic for the methylseq pipeline enhancement New feature or request
#395 opened Apr 2, 2024 by Shaun-Regenbaum 2.7.0
@Shaun-Regenbaum
Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency enhancement New feature or request
#394 opened Apr 1, 2024 by pdemko
1
Latest template merge completely broke dev branch (on AWS + Fusion) bug Something isn't working
#392 opened Mar 27, 2024 by FelixKrueger 2.7.0
1
4
typo in samplesheet in README.md?
#391 opened Mar 25, 2024 by fbnrst
--rrbs and --emseq parameter and argument usage enhancement New feature or request
#389 opened Mar 20, 2024 by deep-buddingcoder
CG CHG and CHH with --comprehensive flag using bismark workflow enhancement New feature or request
#388 opened Mar 13, 2024 by MMJBerger
8
Add gemBS option enhancement New feature or request
#387 opened Mar 6, 2024 by seynard
Create metro map enhancement New feature or request
#383 opened Feb 27, 2024 by matrulda
1
samplesheet input is not detecting entire values in sample column bug Something isn't working
#378 opened Feb 9, 2024 by wvictor14
5
Support for NuGEN Ovation RRBS enhancement New feature or request
#376 opened Jan 19, 2024 by jma1991
2
Add asTair enhancement New feature or request
#374 opened Jan 16, 2024 by bounlu
Add CX report support from bismark_methylation_extractor enhancement New feature or request good first issue Good for newcomers
#372 opened Jan 9, 2024 by Tintest
7
--skip_qualimap parameter to disable qualimap enhancement New feature or request
#367 opened Jan 3, 2024 by adamrtalbot
Scatter CI improvements
#366 opened Dec 22, 2023 by edmundmiller
Missing type field in nextflow_schema.json file bug Something isn't working
#361 opened Dec 1, 2023 by scoughlan2
Error when providing a bwameth index (MethylSeq v2.4.0 and v2.5.0) bug Something isn't working
#353 opened Oct 25, 2023 by bioinfoMMS
1
bwameth index creation fails bug Something isn't working
#352 opened Oct 23, 2023 by FutureFellwalker
7
Pipeline unable to recognise samples processed across multiple lanes bug Something isn't working
#351 opened Oct 22, 2023 by jma1991
2
ProTip! Find all open issues with in progress development work with linked:pr.