Pipeline fails quietly when input fastqs are not found

[SuhasSrinivasan]

Description of the bug

When input fastq files in the sample sheet are not found, the pipeline does not display this error in the console/terminal.
The other initial steps like genome indexing still continue, but the fastq error can only be found in the log file.

It will be helpful if the error is shown in the console so that the user can quickly resolve the issue.

Command used and terminal output

Relevant files

No response

System information

This seems as a better order to list the system information, from lowest to highest level.

Version of nf-core/atacseq: 2.1.2
Nextflow version: v24.10.3
Container engine: Docker 27.4.1
OS: Ubuntu 22.04.5 LTS x86_64
Executor: Local
Hardware: Desktop