Matthias De Smet

I took a look at `qualimap` and found it to be quite slow. Personally, I'm more of a proponent of spreading an analysis horizontally, so I'd use many processes instead...

If there's still interest in this, there's a POC [here](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/blob/dev/subworkflows/local/markdup_parallel/main.nf). It's just missing a small script to merge the metrics before emitting them

Closing this. I'll revisit when I get to it.

ping @michaelgatzen as this might be relevant to your work over at WARP

I don't think this issue has anything to do with this option, or `dragmap`, but stems from `picard`. I suggest you open an issue there. M

Seems to be fixed!

Love this! Exactly what I was looking for 😄

This does throw a `StackOverflowError` for me though

`N E X T F L O W ~ version 22.04.5`

I tried to pretty print the following ``` [DUMP: fastp_trimmed_reads] [['id':'test2', 'samplename':'test2', 'organism':'Sars covid2', 'single_end':false, 'readgroup':['ID':'HK3MMAFX2', 'PU':'HK3MMAFX2', 'PL':'ILLUMINA', 'SM':'test2', 'LB':'test2']], [/Users/matdsmet/Projects/nf-cmgg-preprocessing/work/05/e50b035759d1b21e282b00066c7991/test2_1.fastp.fastq.gz, /Users/matdsmet/Projects/nf-cmgg-preprocessing/work/05/e50b035759d1b21e282b00066c7991/test2_2.fastp.fastq.gz]] ```