[bug] Fails to find FASTQ files when stored on S3

[adamrtalbot]

Description of the bug

viralrecon is affected by nextflow-io/nextflow#4081 this bug.

It looks like the bug is here:

viralrecon/workflows/nanopore.nf

Lines 144 to 145 in 3731dd3

	barcode_dirs = file("${params.fastq_dir}/barcode*", type: 'dir' , maxdepth: 1)
	single_barcode_dir = file("${params.fastq_dir}/*.fastq" , type: 'file', maxdepth: 1)

The error in the log file is here:

Jul-31 02:21:34.846 [main] DEBUG nextflow.Nextflow - No such file or directory: /ngi-igenomes/test-data/viralrecon/minion_test/fastq_pass -- Skipping visit
Jul-31 02:21:34.847 [main] DEBUG nextflow.Nextflow - No such file or directory: /ngi-igenomes/test-data/viralrecon/minion_test/fastq_pass -- Skipping visit
Jul-31 02:21:34.849 [main] ERROR nextflow.Nextflow - Please specify a valid folder containing ONT basecalled, barcoded fastq files generated by guppy_barcoder or guppy_basecaller e.g. '--fastq_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fastq_pass/

Command used and terminal output

nextflow run nf-core/viralrecon -profile test_nanopore,docker --outdir results

### Relevant files

_No response_

### System information

Nextflow: 23.07.0-edge