Nextflow config file issue-CodePudding

Hi Please find below a nf script and a config file. I have run them on two computers. Both computers have nextflow (v 22.04.5) and docker installed. However, one computer shows an error message. Please see the screenshot attached. I checked the log file, and it has just one “command not found”. I was wondering if you could point out what is missing in this computer. Thanks.

nextflow script

#!/usr/bin/env nextflow

//data_location
params.outdir = './results'
params.in = "$PWD/*.fastq"
datasetA = Channel
                .fromPath(params.in)
                .map { file -> tuple(file.baseName, file) }
        

// fastqc

process fastqc {
    tag "${datasetIDA}"
    publishDir "${params.outdir}", mode:'copy'

    input:
    set datasetIDA, file(x) from datasetA

    output:
    file ("${x.baseName}_fastqc.html") into fastqc_ch
            
    script:
    """
    fastqc -Xmx20g $x > ${x.baseName}_fastqc.html
    """
}

config file


process {
    withName:fastqc                            { container = 'staphb/fastqc:latest' }
}

CodePudding user response：

If you're running