If only no file, only one input file , or only read one and not read two is picked up then something is wrong with your input file declaration
- The path must be enclosed in quotes (
'or") - The path must have at least one
*wildcard character. This is even if you are only running one paired end sample.
If the pipeline can't find your files then you will get the following error
ERROR ~ Cannot find any reads matching: *.fastq.gz
Note that if your sample name is "messy" then you have to be very particular with your glob specification. A file name like L1-1-D-2h_S1_L002_R1_001.fastq.gz can be difficult enough for a human to read.
The above information is also covered in the usage README.
The pipeline can't take a list of multiple input files - it takes a glob expression. If your fastq files are scattered in different paths then we recommend that you generate a directory with symlinked files. If running in paired end mode please make sure that your files are sensibly named so that they can be properly paired. See the previous point.
If you still have an issue with running the pipeline then feel free to contact us. Have look at the issue tracker for our repo. Maybe someone has already had the same problem?
Gitter is a chatt client connected to Github, feel free to come in and chat with us; nfcore/smrnaseq Gitter
If you have problems that are related to Nextflow and not our pipeline then check out the Nextflow gitter channel or the google group.