methylseq
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nf-core
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
### Description of feature I know there is a [standard practice](https://nf-co.re/docs/contributing/design_guidelines) for making the schematics for the different nf-core pipelines. I just wanted to know the status of this pipeline's...
### Description of feature Hello, Would it be possible not to instruct Bismark methylation extractor to use both the --comprehensive and --merge_non_CpG flags when specifying --comprehensive to the pipeline ?...
### Description of feature Library preparation kits come with unmethylated and methylated DNA controls that are added to samples (e.g. NEBNext EM-seq). It would be useful to supply methylseq with...
### Description of the bug I am trying to launch a methylseq run using the latest `dev` branch where some (but not a all) samples require merging of technical replicates...
There is an example samplesheet in the README.md: https://github.com/nf-core/methylseq/blob/54f823e102ef3d04077cc091a5ae435519f9923a/README.md?plain=1#L53-L57 I wonder whether there is a typo line 56, because states `SRR389222_sub2` as sample, but the file name contains `SRR389222_sub3`. Also,...
### Description of the bug when (a certain number of?) underscores are used in sample column, sometimes only a substring of the entire value is read in, rather than the...
### Description of feature Hi, I am not a avid user of github and not sure if this is the right place to ask question about a existing feature usage...
### Description of feature Hi, I really like using the nf-core MethylSeq but recently we've been wanting to test gemBS to analyse our RRBS data. We are wondering if this...
### Description of feature Hello, Would it be possible for you to add the ```--CX``` option from the ```bismark_methylation_extractor``` script as you were able to add the ```--comprehensive option``` ?...
