nextflow pipeline for aligning RNA-seq samples to Vitis vinifera transcriptome

bowtie2.nf

#!/usr/bin/env nextflow

params.db = "/nfs3/sonegop/references/PN40024.v4_11_05_21/gene_set/bowtie2_idx/PN40024.v4.1.complete.all.bowtie2"
db = file(params.db)

params.inputDir = "results/fastq"
pairedEndRegex = params.inputDir + "/*_{1,2}.fastq.gz"
/*SERegex = params.inputDir + "/*[!12].fastq.gz"*/
SERegex = params.inputDir + "/*.fastq.gz"

pairFiles = Channel.fromFilePairs(pairedEndRegex)
singleFiles = Channel.fromFilePairs(SERegex, size: 1){ file -> file.baseName.replaceAll(/.fastq/,"") }

singleFiles.mix(pairFiles)
.set { fastqChannel }

indexChannel = Channel
    .fromPath(params.db)
    .ifEmpty { exit 1, "bowtie2 index not found: ${params.db}" }

process alignBowtie2 {
    publishDir 'results/sam', mode: 'copy', overwrite: false

    tag { lane }

    input:
    set val(lane), file(reads) from fastqChannel
    file index from indexChannel.first()

    output:
    file ("${lane}.sam") into samChannel
    file ("${lane}.stats") into statsChannel

    shell:

    def single = reads instanceof Path

    if (!single)
	
    '''
    bowtie2 -p !{task.cpus} --local --sensitive-local -x !{db} -1 !{reads[0]} -2 !{reads[1]} -S !{lane}.sam 2> !{lane}.stats
    '''
    
    else
    '''
    bowtie2 -p !{task.cpus} --local --sensitive-local -x !{db} -U !{reads} -S !{lane}.sam 2> !{lane}.stats
    '''

}


process getCounts {
    publishDir 'results/counts/raw', mode: 'copy', overwrite: false

    input:
    file input from samChannel

    output:
    file "${input.baseName}.counts" into countsChannel

    script:
    "cut -f 3 $input | sort | uniq -c > ${input.baseName}.counts"
}


process sanitizeCounts {
    publishDir 'results/counts/sanitized', mode: 'copy', overwrite: false

    input:
    file input from countsChannel

    output:
    file "${input.baseName}.counts.sanitized" into sanitizedChannel

    script:
    template 'sanitize.sh'
}

nextflow.config

process {
    container = '/nfs3/sonegop/images/bowtie2.4.4.simg'
    executor = 'sge'
    penv = 'smp'
    queue = 'global.q'
    clusterOptions = "-S /bin/bash -cwd -l mf=8G"
    cpus = 6
}

docker {
    enabled = false
}

singularity {
    enabled = true
    autoMounts = true
}

SRR_Acc_List.txt

SRR1631879
SRR1631880
SRR1631881
SRR1631882
SRR1631883
SRR1631884
SRR1631885
SRR1631886
SRR1631887
SRR1631888
SRR1631889
SRR1631890
SRR1631891
SRR1631892
SRR1631893
SRR1631894
SRR1631895
SRR1631896
SRR1631897
SRR1631898
SRR1631899
SRR1631900
SRR1631901
SRR1631902
SRR1631903
SRR1631904
SRR1631905
SRR1631906
SRR1631907
SRR1631908
SRR1631909
SRR1631910
SRR1631911
SRR1631912
SRR1631913
SRR1631914
SRR1631915
SRR1631916
SRR1631917
SRR1631918
SRR1631919
SRR1631920
SRR1631921
SRR1631922
SRR1631923
SRR1631924
SRR1631925
SRR1631926
SRR1631927
SRR1631928
SRR1631929
SRR1631930
SRR1631931
SRR1631932
SRR1631933
SRR1631934
SRR1631935
SRR1631936
SRR1631937
SRR1631938