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23 Open 134 Closed
23 Open 134 Closed
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Issues list

bismark align fails with "java.net.SocketTimeoutException: Read timed out" bug Something isn't working
#507 opened Feb 7, 2025 by trum994
fix bismark_hisat test_full run bug Something isn't working
#500 opened Dec 18, 2024 by sateeshperi
@sateeshperi
add comprehensive param tests
#498 opened Dec 17, 2024 by sateeshperi 3.1.0
1
@sateeshperi
Bismark soft clip --local_alignment True keeps L,value,value bug Something isn't working
#472 opened Nov 27, 2024 by ioannagare
Update multiqc output with bwameth metrics enhancement New feature or request
#463 opened Nov 22, 2024 by sateeshperi
@sateeshperi
Addition of --mergeContext for MethylDackel enhancement New feature or request
#460 opened Nov 21, 2024 by dcarrillox 3.1.0
1
@sateeshperi
5
Add minimap2 as aligner option for Bismark enhancement New feature or request
#455 opened Nov 12, 2024 by FelixKrueger
@sateeshperi
Adding --maxVariantFrac and --minOppositeDepth to MethylDackel (Bwameth option) enhancement New feature or request
#404 opened Jun 18, 2024 by LucaZanella15
1
AS-XS tag missing enhancement New feature or request
#397 opened May 1, 2024 by AndreiWCansor
1
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
@PanosProv
4
--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 3.1.0
@sateeshperi
11
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
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
Option to trim based on Illumina 2 colour chemistry enhancement New feature or request
#240 opened Jul 11, 2022 by npatel-ah
1
Mapping samples to multiple reference fasta dsl2 enhancement New feature or request
#181 opened Nov 30, 2020 by rbpisupati 3.1.0
15
Complexity curve question Further information is requested
#96 opened May 21, 2019 by bazyliszek
5
set picard markduplicates MAX_RECORDS_IN_RAM enhancement New feature or request
#94 opened May 21, 2019 by zchatt
@sateeshperi
Add SNP calling enhancement New feature or request
#65 opened Jan 30, 2019 by ewels
6
ProTip! no:milestone will show everything without a milestone.