Nextflow DSL2 error while constructing BLAST pipeline

Question

''' #! /usr/bin/env nextflow

    nextflow.enable.dsl=2

    println "\nI want to BLAST $params.query to $params.dbDir/$params.dbName using $params.threads CPUs and output it to $params.outdir\n"
  
  
    process runBlast {

    script:
        """
        blastn  -num_threads $params.threads -db $params.dbDir/$params.dbName -query $params.query -outfmt 6 -out input.blastout
        """

    }


    params {
    query = "$PWD/input.fasta"
    dbDir = "$PWD/DB/"
    dbName = "blastDB"
    threads = 2
    outdir = "out_dir"
    }

What workflow {} statement should I add to the main.nf file? The basic BLAST command works, but it does not take additional parameters when added to the command line. The error I get is as follows:

ERROR ~ No such variable: query

Please help if you can, thank you!

I have been following this tutorial: https://bioinformaticsworkbook.org/dataAnalysis/nextflow/02_creatingAworkflow.html#gsc.tab=0

And using this DSL2 documentation for support: https://www.nextflow.io/docs/latest/dsl2.html

Answer 1

Please double check that tutorial. The params scope is meant to be written in a separate file in your projectDir called nextflow.config not in the main.nf. But if you do specify parameters in main.nf, you need to make sure they are set before they are accessed, and I also think that it's not possible to use the scope. Instead write params.query = '$PWD/input.fasta'.

Regarding your question about the workflow: I think that you should first have a look at the concept of Channels instead of using the process as written in any workflow. After quickly scrolling through that tutorial, I find it very difficult to get what nextflow really is about and only throws snippets of code that don't work out of the box at the readers. Also, I find it not very helpful, that it introduces parameters very early, but not process inputs/outputs and does not mention Channels before section 9. Maybe you should start with the basic concept from the official docs instead? https://www.nextflow.io/docs/latest/basic.html