Removed custom cat fastq module as nf-core one is fixed

// Import generic module functions

include { initOptions; saveFiles } from './functions'

params.options = [:]

options        = initOptions(params.options)

/*

 * Concatenate FastQ files

 */

process CAT_FASTQ {

    tag "$meta.id"

    label 'process_low'

    publishDir "${params.outdir}",

        mode: params.publish_dir_mode,

        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'merged_fastq', publish_id:meta.id) }

    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)

    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"

    } else {

        container "biocontainers/biocontainers:v1.2.0_cv1"

    }

    input:

    tuple val(meta), path(reads)

    output:

    tuple val(meta), path("*.merged.fastq.gz"), emit: reads

    script:

    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

    readList     = reads.collect{it.toString()}

    if (!meta.single_end) {

        if (readList.size > 2) {

            def read1 = []

            def read2 = []

            readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }

            """

            cat ${read1.sort().join(' ')} > ${prefix}_1.merged.fastq.gz

            cat ${read2.sort().join(' ')} > ${prefix}_2.merged.fastq.gz

            """

        } else {

            """

            ln -s ${reads[0]} ${prefix}_1.merged.fastq.gz

            ln -s ${reads[1]} ${prefix}_2.merged.fastq.gz

            """

        }

    } else {

        if (readList.size > 1) {

            """

            cat ${readList.sort().join(' ')} > ${prefix}.merged.fastq.gz

            """

        } else {

            """

            ln -s $reads ${prefix}.merged.fastq.gz

            """

        }

    }

}

 * MODULES

 */

include { INPUT_CHECK                    } from "../subworkflows/local/input_check"                          addParams( options: [:]                                        )

include { CAT_FASTQ                      } from "../modules/local/cat_fastq"                                 addParams( options: cat_fastq_options                          )

include { CAT_FASTQ                      } from "../modules/nf-core/modules/cat/fastq/main"                  addParams( options: cat_fastq_options                          )

include { BEDTOOLS_GENOMECOV_SCALE       } from "../modules/local/bedtools_genomecov_scale"                  addParams( options: modules["bedtools_genomecov_bedgraph"]     )

include { SEACR_CALLPEAK as SEACR_NO_IGG } from "../modules/local/seacr_no_igg"                              addParams( options: modules["seacr"]                           )

include { AWK as AWK_NAME_PEAK_BED       } from "../modules/local/awk"                                       addParams( options: modules["awk_name_peak_bed"]               )