Hi everyone,

I am trying to learn making workflows using Nextflow. I want to make an ATAC Seq workflow. I have 2 set of paired end ATAC Seq data.

First i perform adapter trimming using trimgalore. The ouputs of trimGalore consist of the two trimmed fqs for each set.

Then i want those trimmed fqs to be used as input in bowtie2, but i havent found a way of transforming pairedTrimmedCh to paired file channel in order to run the alignment proccess.

Any help?

Thanks in advance!

#!/usr/bin/env nextflow

params.reads = "./*{1,2}.fastq"
params.outdir = "bams"
params.INDEX = "path_to_index"
params.cpus = 10

log.info """\

    A T A C S E Q - N F   P I P E L I N E
    ===================================
    Genome: ${params.INDEX}
    reads        : ${params.reads}
    outdir       : ${params.outdir}
    """
    .stripIndent(true)



process trimReads {

    publishDir "$params.outdir/", mode: 'copy'
    input:
    tuple val(sampleid), path(reads)

    output:
    path "./trimmed/" 

    script:
    """
TrimGalore-0.6.7/trim_galore --cores 7 --paired --no_report_file ${reads[0]} ${reads[1]}  -o ./trimmed/

    """
}


process alignment {
    publishDir "$params.outdir/", mode: 'copy'

    input:
    tuple val(sampleid), path(reads)

    output:
    path "${sampleid}.mm10.sorted.bam", emit: bams
    path "${sampleid}.mm10.sorted.bam.bai"

    script:
    """
    bowtie2 --local -X 2000 -p ${params.cpus} -x ${params.INDEX} -1 ${trimmed_reads[0]} -2 ${trimmed_reads[1]} | samtools view -b -h -S -q 10 -f 0x2 | samtools sort -@ ${params.cpus}  > ${sampleid}.mm10.sorted.bam
    samtools index ${sampleid}.mm10.sorted.bam
    """
}

workflow {
    // Create a channel with fastqs. If paired-end, use .fromFilePairs
    Channel
        .fromFilePairs(params.reads, checkIfExists: true)
        .set { read_ch }

    pairedTrimmedCh = trimReads(read_ch).groupTuple()

    align_ch = alignment(pairedTrimmedCh)
}