Nextflow No such variable: id

Question

I'm trying to perform my first code with Next-flow, im introducing 2 paired reads and I want to execute the bbduk function. I don't know why my code didn't works.

I tryed the following code:

  #!/usr/bin/env nextflow


/*
 * Pipeline Metagenomics, conda ambient Metagenomics_Nextflow
 */

 nextflow.enable.dsl=2 // Nextflow version

params.fq1 = "$HOME/../*{1}.fq.gz" // Can be modified in the script with the --fq1 <value> command
params.fq2 = "$HOME/..//*{2}.fq.gz" // Can be modified in the script with the --fq2 <value> command
/*
 * params.out = 'OTU.tsv'       // result file
 * params.databaseHuman = "$baseDir/Database/GRCh38" // 
 */

/*
 * Check the quality of raw sequences
 */

 process BBduk {

    input:
        tuple val(meta), path(reads)
    tag {meta.id}

    output:
        tuple val(meta), path('*.fq.gz'), emit: reads
        tuple val(meta), path('*.log'), emit: log
    
     script:
        def prefix = file("${meta.id}")
        def raw      = "in1=${reads[0]} in2=${reads[1]}"
        def trimmed  = "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
        """
        echo(${prefix})
        echo(${raw})
        echo(${trimmed})
        bbduk.sh \\
        $raw \\
        $trimmed \\
        qtrim=r trimq=10 minlen=100 \\
        &> ${prefix}.bbduk.log
        """

 }
/*
* Workflow
*/
workflow {
sequences = Channel.fromFilePairs( [params.fq1,params.fq2] )
println "Performing Quality control and triming from $sequences" 
    BBduk(sequences)
}   

The code produce the following error in terminal.

 ERROR ~ Error executing process > 'BBduk (1)'

Caused by:
  No such variable: id -- Check script 'Workflow_Clean_Human_DNA.nf' at line: 34

Source block:
  def prefix = file("${meta.id}")
  def raw      = "in1=${reads[0]} in2=${reads[1]}"
  def trimmed  = "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
  """
          echo(${prefix})
          echo(${raw})
          echo(${trimmed})
          bbduk.sh \\
          $raw \\
          $trimmed \\
          qtrim=r trimq=10 minlen=100 \\
          &> ${prefix}.bbduk.log
          """

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

The idea of the code is to perform a bbduk algorithm into raw reads, I tried to perform a duple to work. I wan't to do it in next flow because the idea is chain the output with other algorithm

Thanks!

Answer 1

The fromFilePairs factory method emits tuples in which the first element is the grouping key (and the second element is the list of matching files). It is a simple String (java.lang.String), not a Map of meta data. I think all you need is something like:

params.reads = './*_{1,2}.fq.gz'


process BBduk {

    tag { sample_id }

    input:
    tuple val(sample_id), path(reads, stageAs: 'reads/*')

    output:
    tuple val(sample_id), path("${sample_id}_{1,2}.fq.gz"), emit: reads
    tuple val(sample_id), path("${sample_id}.bbduk.log"), emit: log

    script:
    def (fq1, fq2) = reads

    """
    bbduk.sh \\
        in1="${fq1}" \\
        in2="${fq2}" \\
        out1="${sample_id}_1.fq.gz" \\
        out2="${sample_id}_2.fq.gz" \\
        qtrim=r \\
        trimq=10 \\
        minlen=100 \\
        &> "${sample_id}.bbduk.log"
    """
}

workflow {

    reads = Channel.fromFilePairs( params.reads )

    BBduk( reads )
}

Note that by staging the files in a subdirectory (using stageAs: 'reads/*'), we ensure we don't accidentally clobber our input files in the working directory.