fq.gz not staged correctly when skipping demultiplexing

[CormacKinsella]

Description of the bug

If demultiplexing is skipped qcat.nf isn't run.

Nanoplot for example expects .fastq.gz extensions or it will evaluate $input_file to an empty string.

If users provide fq.gz files and qcat isn't run, the file is staged as is and nanoplot tasks fail, rather than being processed into a fastq.gz.

Command used and terminal output

nextflow main.nf -profile test,singularity --skip_demultiplexing --input  samplesheet.csv

Requires a demultiplexed fq.gz input.

Relevant files

No response

System information

No response