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. - When using the pipeline with paired end data, the path must use
{1,2}or{R1,R2}notation to specify read pairs. - If you are running Single end data make sure to specify
--singleEnd
If the pipeline can't find your files then you will get the following error
ERROR ~ Cannot find any reads matching: *{1,2}.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. Specifying *{1,2}*.gz wont work give you what you want Whilst *{R1,R2}*.gz will.
The pipeline can't take a list of multiple input files - it takes a glob expression. If your input 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 pipeline website to find out how.
If you have problems that are related to Nextflow and not our pipeline then check out the Nextflow gitter channel or the google group.
It is possible that you don't have execution rights for scripts in the bin/ directory after downloading from GitHub. In that case, you simply have to set the correct rights for these scripts manually and run again (or resume).