nf-core methylseq issues

nf-core / methylseq

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

https://nf-co.re/methylseq

MIT License

137 stars 133 forks source link

issues

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Newest Most commented Recently updated Oldest Least commented Least recently updated

samplesheet handling: different path + same filename gives an error

#407 AdrijaK opened 3 weeks ago
0
Multiple issues in the pipeline

#406 gevro closed 3 weeks ago
1
Bwameth vs bismark

#405 gevro opened 1 month ago
0
Adding --maxVariantFrac and --minOppositeDepth to MethylDackel (Bwameth option)

#404 LucaZanella15 opened 1 month ago
0
fix usage of Fasta references for bwameth / samtools faidx

#403 maxulysse closed 1 month ago
1
Write tests for samplesheet sample merging/grouping

#402 edmundmiller opened 2 months ago
0
Fix/sample merge

#401 sateeshperi closed 2 months ago
1
fix branching of single and multiple

#400 sateeshperi closed 2 months ago
1
Important! Template update for nf-core/tools v2.14.1

#399 nf-core-bot closed 2 months ago
1
Important! Template update for nf-core/tools v2.14.0

#398 nf-core-bot closed 2 months ago
1
AS-XS tag missing

#397 AndreiWCansor opened 2 months ago
0
bwameth pipeline skipping all bwameth steps when --fasta, --fasta_index, and --bwa_meth_index are provided.

#396 drothen15 opened 3 months ago
2
Schematic for the methylseq pipeline

#395 Shaun-Regenbaum opened 3 months ago
0
Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency

#394 pdemko opened 3 months ago
1
test(#392): Add boilerplate for tests

#393 edmundmiller closed 2 months ago
1
Latest template merge completely broke dev branch (on AWS + Fusion)

#392 FelixKrueger opened 3 months ago
4
typo in samplesheet in README.md?

#391 fbnrst opened 4 months ago
0
Bump preseq

#390 ewels closed 3 weeks ago
2
--rrbs and --emseq parameter and argument usage

#389 deep-buddingcoder opened 4 months ago
0
CG CHG and CHH with --comprehensive flag using bismark workflow

#388 MMJBerger opened 4 months ago
8
Add gemBS option

#387 seynard opened 4 months ago
0
remove duplicate section from usage.md

#386 fbnrst closed 4 months ago
1
remove duplicate section in usage.md

#385 fbnrst closed 4 months ago
1
Important! Template update for nf-core/tools v2.13.1

#384 nf-core-bot closed 4 months ago
1
Create metro map

#383 matrulda opened 4 months ago
1
fix annoying PRESEQ failure

#382 bounlu closed 4 months ago
8
Fix/samplename join

#381 sateeshperi closed 5 months ago
1
Important! Template update for nf-core/tools v2.13

#380 nf-core-bot closed 4 months ago
1
Support for NuGen Ovation RRBS libraries

#379 jma1991 opened 5 months ago
2
samplesheet input is not detecting entire values in sample column

#378 wvictor14 opened 5 months ago
6
Important! Template update for nf-core/tools v2.12

#377 nf-core-bot closed 5 months ago
1
Support for NuGEN Ovation RRBS

#376 jma1991 opened 6 months ago
2
add missing comma to awstestfull yml

#375 sateeshperi closed 6 months ago
1
Add `asTair`

#374 bounlu opened 6 months ago
0
Fix CI rate-limit

#373 edmundmiller opened 6 months ago
2
Add CX report support from bismark_methylation_extractor

#372 Tintest opened 6 months ago
7
post-release dev bump version and snapshots

#371 sateeshperi closed 6 months ago
1
Use install-gh-release GitHub Action

#370 edmundmiller closed 6 months ago
2
Dev -> Master 2.6.0

#369 edmundmiller closed 6 months ago
2
Important! Template update for nf-core/tools v2.11.1

#368 sateeshperi closed 6 months ago
1
--skip_qualimap parameter to disable qualimap

#367 adamrtalbot opened 6 months ago
0
Scatter CI improvements

#366 edmundmiller opened 7 months ago
0
Important! Template update for nf-core/tools v2.11

#365 nf-core-bot closed 6 months ago
2
Add bwameth test config

#364 scoughlan2 closed 6 months ago
3
Correct documentation to explain minimal inputs for bwa-meth subworkflow

#363 scoughlan2 closed 5 months ago
4
No groups

#362 edmundmiller closed 7 months ago
2
Missing type field in nextflow_schema.json file

#361 scoughlan2 opened 7 months ago
0
ERROR ~ fromIndex = -1

#360 Adrian-Zet closed 6 months ago
6
Fix expansion of ignore_r1 parameters in modules.config

#359 noecochetel closed 8 months ago
3
Parameters ignore_r1 for methylationextractor not expanded

#358 noecochetel closed 8 months ago
0