TheodoreMarkulin

### Description of feature # What is being proposed? Currently the base sample sheet template uses: `sample`, `fastq_1`, `fastq_2`, and `single_end`. I would like to propose adding a 5th column...

## 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...

## 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'...

Sample Sheets >2048 character give Error: Could not determine delimiter (DSL2)

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## 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...