Nextflow report an error : No such variable : from

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I'm trying to learn nextflow but it's not going very well. I used NGS-based double-end sequencing data to build an analysis flow from fastq files to vcf files using Nextflow. However I got stuck right at the beginning, as shown in the code. The first process soapnuke works fine, but when passing the files from the channel (clean_fq1 \ clean_fq2) to the next process there is an ERROR: No such variable: from. As shown in the figure below. What should I do? Thanks for a help.

enter image description here

params.fq1 = "/data/mPCR/220213_I7_V350055104_L3_SZPVL22000812-81/*1.fq.gz"
params.fq2 = "/data/mPCR/220213_I7_V350055104_L3_SZPVL22000812-81/*2.fq.gz"
params.index = "/home/duxu/project/data/index.list"
params.primer = “/home/duxu/project/data/primer_*.fasta"
params.output='results'

fq1 = Channel.frompath(params.fq1)
fq2 = Channel.frompath(params.fq2)
index = Channel.frompath(params.index)
primer = Channel.frompath(params.primer)

process soapnuke{
    conda'soapnuke'
    tag{"soapnuk ${fq1} ${fq2}"}
    publishDir "${params.outdir}/SOAPnuke", mode: 'copy'
    input:
        file rawfq1 from fq1
        file rawfq2 from fq2    

    output:
        file 'clean1.fastq.gz' into clean_fq1
        file 'clean2.fastq.gz' into clean_fq2
    
script:
    """
    SOAPnuke filter -1 $rawfq1 -2 $rawfq2 -l 12 -q 0.5 -Q 2 -o . \
        -C clean1.fastq.gz -D clean2.fastq.gz
    """
}

I get stuck on this:

process barcode_splitter{
    conda'barcode_splitter'
    tag{"barcode_splitter ${fq1} ${fq2}"}
    publishDir "${params.outdir}/barcode_splitter", mode: 'copy'
    input:
        file split1 from clean_fq1
        file split2 from clean_fq2
        index from params.index

    output:
       file '*-read-1.fastq.gz' into trimmed_index1
       file '*-read-2.fastq.gz' into trimmed_index2

    script:
    """
    barcode_splitter --bcfile $index $split1 $split2  --idxread 1 2 --mismatches 1 --suffix .fastq --gzipout
    """
}
nextflow
1 Answers

The code below will produce the error you see:

index = Channel.fromPath( params.index )

process barcode_splitter {
     ...

     input:
     index from params.index

     ...
}

What you want is:

index = file( params.index )

process barcode_splitter {
     ...

     input:
     path index

     ...
}

Note that when the file input name is the same as the channel name, the from channel declaration can be omitted. I also used the path qualifier above, as it should be preferred over the file qualifier when using Nextflow 19.10.0 or later.

You may also want to consider refactoring to use the fromFilePairs factory method. Here's one way, untested of course:

params.reads = "/data/mPCR/220213_I7_V350055104_L3_SZPVL22000812-81/*_{1,2}.fq.gz"
params.index = "/home/duxu/project/data/index.list"
params.output = 'results'

reads_ch = Channel.fromFilePairs( params.reads )
index = file( params.index )


process soapnuke {

    tag { sample }

    publishDir "${params.outdir}/SOAPnuke", mode: 'copy'
    conda 'soapnuke'

    input:
    tuple val(sample), path(reads) from reads_ch

    output:
    tuple val(sample), path('clean{1,2}.fastq.gz') into clean_reads_ch

    script:
    def (rawfq1, rawfq2) = reads

    """
    SOAPnuke filter \\
        -1 "${rawfq1}" \\
        -2 "${rawfq2}" \\
        -l 12 \\
        -q 0.5 \\
        -Q 2 \\
        -o . \\
        -C "clean1.fastq.gz" \\
        -D "clean2.fastq.gz"
    """
}

process barcode_splitter {

    tag { sample }

    publishDir "${params.outdir}/barcode_splitter", mode: 'copy'
    conda 'barcode_splitter'

    input:
    tuple val(sample), path(reads) from clean_reads_ch
    path index

    output:
    tuple val(sample), path('*-read-{1,2}.fastq.gz') into trimmed_index

    script:
    def (splitfq1, splitfq2) = reads

    """
    barcode_splitter \\
        --bcfile \\
        "${index}" \\
        "${split1}" \\
        "${split2}" \\
        --idxread 1 2 \\
        --mismatches 1 \\
        --suffix ".fastq" \\
        --gzipout
    """
}
user_7518630
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