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29 Open 106 Closed
29 Open 106 Closed
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Issues list

mv bismark, bwameth sub-wf from pipeline local to nf-core enhancement New feature or request
#453 opened Nov 9, 2024 by sateeshperi 2.8.0
@sateeshperi
integrate parabricks/fq2bammeth module enhancement New feature or request
#447 opened Oct 25, 2024 by sateeshperi 2.8.0
1
Command error: ln: Sample_Name.fastq.gz: File exists
#425 opened Oct 10, 2024 by OliverH96
Is the cytosine report (.CpG_report.txt.gz) analyzed from deduplicated data?
#423 opened Oct 9, 2024 by gevro
Pipeline requires 72GB of RAM, even to test.
#408 opened Jul 26, 2024 by mpiersonsmela
3
Bwameth vs bismark enhancement New feature or request good first issue Good for newcomers
#405 opened Jun 23, 2024 by gevro
@sateeshperi
1
Adding --maxVariantFrac and --minOppositeDepth to MethylDackel (Bwameth option) enhancement New feature or request
#404 opened Jun 18, 2024 by LucaZanella15
AS-XS tag missing enhancement New feature or request
#397 opened May 1, 2024 by AndreiWCansor
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
2
--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
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
1
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
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 2.7.0
2
Refactor kit processing to be maintainable
#338 opened Aug 25, 2023 by edmundmiller
1
Add --skip_fastqc option enhancement New feature or request
#327 opened Jun 20, 2023 by bounlu
Additional downstream processes written in DSL1 -- UPGRADE now to DSL2 enhancement New feature or request
#283 opened Dec 6, 2022 by Jani-94
@Jani-94
2
Add support for Bismark minimap2 enhancement New feature or request
#257 opened Nov 8, 2022 by ewels 3.0.0
1
Option to trim based on Illumina 2 colour chemistry enhancement New feature or request
#240 opened Jul 11, 2022 by npatel-ah
Mapping samples to multiple reference fasta dsl2 enhancement New feature or request
#181 opened Nov 30, 2020 by rbpisupati 3.0.0
15
Preseq failing most of the time help wanted Extra attention is needed
#161 opened May 29, 2020 by ewels
1
13
Complexity curve question Further information is requested
#96 opened May 21, 2019 by bazyliszek
5
ProTip! no:milestone will show everything without a milestone.