methylseq
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nf-core
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
### Description of the bug Hi - thanks for all your work on the pipeline. I have a recurrent issue which is easy to overcome but I presume is caused...
### Description of the bug "type": "string" should be above the line at https://github.com/nf-core/methylseq/blob/master/nextflow_schema.json#L412 ### Command used and terminal output _No response_ ### Relevant files _No response_ ### System information...
### Description of the bug I am running into an error regarding bwameth indexing/aligning. I am trying to get the bwameth pipeline to work with an existing bwameth index. Looks...
Bismark now supports using minimap2 for alignment. We should add another `params.aligner` option for this.
@FelixKrueger we should make a json or yaml or csv or something of the table linked above, and then parse it either in the methylseq pipeline, or get it baked...
### Description of the bug when the following command is run the test profile fails nextflow run nf-core/methylseq \ -profile test,singularity \ --outdir /projects/team/bioinformatics/nextflow_testing \ --em_seq ### Command used and...
I want to extract **deduplicated and sorted** bam file from the pipeline by using the `Bismark` aligner. When I use `--save_align_intermeds` flag, `SAMTOOLS_SORT` module writes the sorted bam file to...
### Description of feature It would be nice to have the option `--skip_fastqc` just like in other pipelines e.g. [`rnaseq`](https://nf-co.re/rnaseq/3.12.0/parameters#skip_fastqc). Sometimes FastQC reports are already available from a previous analysis...
### Description of the bug There's way too many weird conflicts ### Command used and terminal output _No response_ ### Relevant files _No response_ ### System information _No response_
### Description of feature Combo'd with the "changes" I think we can finally get tests that only run on changes that might affect them! I'll get to this in a...