methylseq
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nf-core
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Version `2.5` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...
dsl2 port
Continuation of https://github.com/nf-core/methylseq/pull/182 (now from a dedicated branch) :warning: Breaking change: The pipeline now requires a sample sheet to be passed to the pipeline with `--input`: | sample | fastq_1...
Hello, Thank you for amazing work on this pipeline, it's very comprehensive. I am wondering if there is any way to specify `--2colour` / `--nextseq` flag during trimming step. I...
## Description of the bug Pipeline fails when given a preindexed bwameth index. This is due to the Collect Software Versions step at the end of the `bwameth.nf` script. When...
It is desired to merge files from multiple lanes belonging to the same sample. Often the samples are sequenced in multiple lanes and this indeed speeds up the alignment step,...
## Description of the bug In the DSL2 branch, when using the `--methylkit` parameter in conjunction with methyldactyl the pipeline fails. This appears to be due to an 'either or'...
## Description of the bug When using a particularly large sample sheet the `sniff_format` function is unable to determine the format of the sample sheet and returns an error. This...
## DSL2 does not allow for using already indexed custom genome I use a custom variation of GRCh38 that includes control sequences. It takes a while to index the entire...
Going to setup pytest to track tests and results to verify the DSL2 conversion, so we can have confidence in the reproduction and know of any changes. Going to avoid...
## Check Documentation I have checked the following places for your error: - [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [X] [nf-core/methylseq pipeline documentation](https://nf-co.re/nf-core/methylseq/usage) ## Description of the bug When running on...