methylseq
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nf-core
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...
### Description of the bug Hi, I am reading through methylseq v4.2.0 tutorial (https://nf-co.re/methylseq/4.2.0/parameters/) and I found there are two contradictory explanations about option "--zymo". One says 10bp is trimmed...
### Description of the bug [This line](https://github.com/nf-core/methylseq/blob/4415e90a60faba40ccefd4c847666d28688a86ee/modules/nf-core/bismark/summary/main.nf#L36) seems to cause the issue. Because `bam` is specified as a `value` channel rather than `path`. ``` -[nf-core/methylseq] Pipeline completed with errors- ERROR...
### Description of the bug The workflow terminates after the TrimGalore step with a successful exit status, but no alignment files are generated. TrimGalore completes normally and its output files...
### Description of the bug In methylseq v4.1.0 noticed something unclear in the documentation. In the main usage guide under *Parameters*, it states: > “It is mandatory to provide `--fasta`...
The naming scheme for the "genome" field in the samplesheet is overly strict and forbids using paths containing a slash. It seems sensible to allow more locations than the current...
### Description of feature For the targeted sequencing analysis, I have multiple target regions for different features and I want to check metrics for them separately. I want to provide...
### Description of the bug Hello community! I have been trying to run the option --local_alignment as True to enable soft clipping and get this error: In Bowtie 2 --local...
### Description of feature As requested by @sateeshperi, it would be nice to support minimap2 as alternative aligner for Bismark. Here are the options that are currently supported: **MINIMAP2-SPECIFIC OPTIONS:**...
