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34 Open 136 Closed
34 Open 136 Closed
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Issues list

Update fq2bammeth enhancement New feature or request
#536 opened May 24, 2025 by GallVp
1
@GallVp
GPU test on singularity fails bug Something isn't working
#532 opened May 24, 2025 by sateeshperi
1
switch CI to runson enhancement New feature or request
#531 opened May 24, 2025 by sateeshperi
1
@GallVp
"Permission denied" error.
#529 opened May 23, 2025 by edmundmiller
1
@edmundmiller
PARABRICKS_FQ2BAMMETH fails with CPU OOM bug Something isn't working
#528 opened May 15, 2025 by GallVp
1
@GallVp
1
Running in -stub mode fails for BISMARK_SUMMARY bug Something isn't working
#527 opened May 9, 2025 by bounlu
Pixel distance in Picard mark duplicates bug Something isn't working
#526 opened May 6, 2025 by trombitomi
Remove --use_gpu parameter enhancement New feature or request
#520 opened Apr 15, 2025 by GallVp
1
@GallVp
JSON schema: Methylseq
#513 opened Mar 25, 2025 by jen-reeve
15 tasks
--targeted analysis enhancement New feature or request WIP Work in progress
#511 opened Mar 24, 2025 by dcarrillox
@dcarrillox
3
Help with Sample Sheet Preparation for Methyl-seq (S4 Illumina EM-seq) enhancement New feature or request
#510 opened Mar 19, 2025 by CHOWDHURY098
1
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
8
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
5
--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/rastair enhancement New feature or request
#374 opened Jan 16, 2024 by bounlu
1
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