nf-core
Add fastq preprocessing to the pipeline
Description Currently, there is no pre-processing of the sequencing files and we would like to add this. There is a paper that describes a lncRNA pipeline that includes pre-processing that we can use as an example.
Which part would you like to add? The Fastp and bbmap step? For this issue, this would include adapter trimming and rRNA removal.
@SchreiberM It would be good to include both adapter trimming+quality filtering and the rRNA removal step.
I think that this subworkflow would be ideal since it does the needed steps mentioned: https://nf-co.re/subworkflows/fastq_qc_trim_filter_setstrandedness/
It also works with the ch_fastq that we have created for the samplesheet
