methylseq
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nf-core
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
My attempt at getting the DSL2 port of this pipeline over the line. A lot has changed since @phue originally worked on this. For starters, the DSL2 template is now...
## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...
It would be nice to be able to have the option of calling variants from bisulfite data. It shouldn't be too tricky to add [Bis-SNP](https://github.com/dnaase/Bis-tools) or something similar as a...
Anyone running the pipeline will be familiar with this log message: ``` terminated with an error status (1) -- Error is ignored. ``` Preseq has a history of failing a...
# nf-core/methylseq pull request This is a continuation-improved PR of this PR: https://github.com/nf-core/methylseq/pull/147 ## PR checklist - [x] This comment contains a description of changes (with reason) - [x] Ensure...
Hello, I am currently running nf-core/methylseq with bwameth/MethylDackel option to generate methytKit-compartible methylation files. However, I could not find the location of the generated files in the output directory (outDir)....
Hi, I was thinking of adapting this pipeline to take care of multiple reference genomes. Something like each sample would be aligned to different reference fasta file. Any votes for...
I have a problem with qualimap, it fails with big bam files, no matter how much memory and CPUs I give. (I can't give more then 256G due to cluster...
1. Looking into complexity curve. Could it be that for PE reads we actually need to add the `-P` parameter in preseq? This was not detected in the pipeline automatically....
Hello, Thank you again for this great tool. Would it be possible to set set picard markduplicates `MAX_RECORDS_IN_RAM`? I have noticed that running large `.bam` files (>200Gb) this step is...
