Read Input Parameter as Folder

[apeltzer]

params.reads should only specify the folder, but only files like *_L001_R{1,2}_001.fastq.gz are chosen (QIIME2 PE input requires *_L001_R{1,2}_001.fastq.gz format, so this is required anyway)

[d4straub]

This doesnt work with 1.0dev. I still need to define --reads "data/*_L001_R{1,2}_001.fastq.gz"
In branch dev I somehow cant find the changes you made in main.nf, but the changes in nextflow.config are present.

[d4straub]

also, all --singleEnd options would not work at the moment. qiime import is expecting paired end, we would need to implement single end processing in several steps.

[apeltzer]

I created a separate Issue for the second point. For the first, this is specified as folder + pattern and should take this automatically into account. Will have a look later after meeting.

[d4straub]

works