error: No input FASTQs were found for the requested parameters.
for several hours now. In my case the file names, the file path and the command were all fine. Finally what solved the issue for me was to move the fastq.gz files into a seperate folder that only contained fastq.gz files. The original folder had some other files in it (md5, fastqc output, etc.). Not sure why this was a problem for the pipeline, but make sure to give this a try if you run into similar trouble.
Thank you for your contributions.
Finally gotten it to work - the codes below work fine. Turns out it was the space after --sample= as genomax astutely pointed out. Hoci also made a great point about naming of the samples which must be strictly adhered.
For those who might be wondering, fastq or fastq.gz will work just fine. If you are at working directory, --fastqs=. would also work. (So far, the header of my fastq files had not produced any errors, but I'll keep updated on the output.)