I have created a nextflow pipeline to complete hisat2 alignment on a set of fastq.gz files found in the flist_parsed.txt file. When I attempt to have these fastq files run in the pipeline, i receive an error:
I assume the pipeline is not recognizing the fastq files. I'm not sure how to input the fastq, with each fastq in the file having a different name in my pipeline to have the pipeline be successful.
I'd agree with you, but just to clarify. The fact that you actually used
path(fastq1), named the input file
fastq1in the script section of the process, which is why Nextflow is complaining about
No such variable: fastq1. And as Mensur said, issue is the same for
I'd recommend watching the training that happened last week and is available on youtube: https://www.youtube.com/watch?v=nzR8DRq13nE