Thank you Matthias! Leaving

genome

empty and setting

fasta

, I'm now getting this one:

WARN: The following invalid input values have been detected:

* --markdown_path: /mnt/biggley/home/slava/projects/leancage_dev/cageseq/assets/cager_report.Rmd


WARN: Found the following unidentified headers in /mnt/biggley/home/slava/projects/leancage_dev/test_samplesheet/samplesheet.csv:
        - single_end

Reading in samplesheet
Creating channel from samplesheet
Initializing channels
ERROR ~ Reference genome FASTA file (--genome) or genome index (--index) should be specified.

 -- Check '.nextflow.log' file for details