Hi All, Thanks so much for this pipeline, I'm looking forward to using it! I downloaded fastq files from SRA, which aren't gzipped. Is it possible to run the pipeline with un-gzipped files? I got an error that the validation of pipeline parameters failed, because they didn't end in .gz; I'm looking through the documentation and nothing explicitly says they need to be gzipped, and my understanding is that other nf-core pipelines can accept non-gzipped files. Is there some kind of flag I can pass so that I don't need to additional gzip all the files when they're already uncompressed? Thanks!

The

schema_input.json

is responsible for this pattern:

"fastq_1": {
                "type": "string",
                "format": "file-path",
                "exists": true,
                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
            },

So I guess you'll have to compress them first

I just zipped them, thanks!