methylseq
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nf-core
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
### Description of feature Already forked from methylseq (written in DSL1) and added the following: 1. additional methylation calling with cgmaptools and general statistics (plots and tables) using cgmaptools. 2....
### Description of feature Dear nf-core team We tried methylseq which's been brilliant. One specific question is about AS-XS tag as they were missing in our output bam file. I...
### Description of the bug Hi all, I have encountered a buggy behaviour in samplesheet processing: My samplesheet has specified absolute paths to different files (`/path/to/run_01/` and `/path/to/run_02/`) with same...
Hi, I'm curious if you have recommendations on which aligner/process is best to use in specific situations? Or is it purely just use user preference?
### Description of feature Hi all, I think that adding the possibility to provide the `--maxVariantFrac option` (and its `--minOppositeDepth` counterpart, by default set to 0) would be of great...
### Description of the bug On my university's cluster, users are penalized (with priority reduction) for requesting more RAM than they actually use. So the fact that the pipeline requires...
### Description of feature * integrate [parabricks/fq2bammeth](https://github.com/nf-core/modules/tree/master/modules/nf-core/parabricks/fq2bammeth) * Add `use_gpu` logic to workflow for bwameth
I'm running methylseq v2.6.0 on some RRBS data, but am having some trouble. I've been getting the error: ERROR ~ Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE (MBioS_BACD)' Caused by: Process `NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE...
Hi, Question: Is the cytosine report (.CpG_report.txt.gz) analyzed from deduplicated data? Seems like it from the code, but wanted to confirm definitively. Thanks