Error "cat: '*.fastq.gz': No such file or directory" when adding additional Guppy parameters

[pcantalupo]

Hello, I tried to run the pipeline (-r dev) into accepting additional Guppy parameters so that Guppy would perform Qscore filtering of fastq into "pass" and "fail" groups. However the pipeline failed with this error Command error: cat: '*.fastq.gz': No such file or directory

The command line that I used was nextflow run nf-core/nanoseq --input samplesheet.csv --protocol cDNA --input_path ./fast5_pass --flowcell 'FLO-MIN106 --qscore_filtering --min_qscore 7' --kit SQK-DCS109 --skip_demultiplexing --skip_quantification -config myconfig.config -profile singularity -r dev

The contents of my sample sheet and the pipeline_report.txt are listed in this GIST. When I look in the nextflow work directory used by Guppy, I see that it is properly separating the failed fastq from the passed fastq into their respective fail and pass directories. But the pipeline doesn't realize that the *fastq.gz files are in the pass directory and not in the current directory; hence the cat error.