BED file for use with --snpcapture_bed not recognized

[meganemichel]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/eager pipeline documentation
  - nf-core/eager FAQ/troubleshooting can be found here

Description of the bug

Bed files supplied via the --snpcapture_bed flag are not properly staged. This results in qualimap throwing a file not found error when trying to execute bamqc.

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/eager -r 2.4.2 -profile eva,archgen,test --snpcapture_bed '/mnt/archgen/users/michel/plasmodium/99-references/falciparum/mitochondrion/LR605957.1_0based_snpcap.bed'
2. See error: ERROR: input region gff file not found