FastQ file not recognized by hisat2 allignment

Question

[selenaajohn]

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.

Answer 1

[Mensur Dlakic]

No such variable: fastq1

Error messages don't come any clearer than this. Your script is expecting a variable named fastq1 to be used in this line:

hisat2 -p 16 -x genome -1 ${fastq1} ...

and you haven't defined a variable by that name - or fastq2 or baseName, for that matter.

Based on this question and the one you asked previously, I suggest that you spend some time to understand bash - topics like PATH, variables, looping - before working with Nextflow scripts.

[Maxime Garcia]

I'd agree with you, but just to clarify. The fact that you actually used path("fastq1") instead of path(fastq1), named the input file fastq1 in 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 fastq2.

I'd recommend watching the training that happened last week and is available on youtube: https://www.youtube.com/watch?v=nzR8DRq13nE