deleted local get_chrom_sizes module

// Import generic module functions

include { initOptions; saveFiles; getSoftwareName; getProcessName } from './common/functions'

params.options = [:]

options        = initOptions(params.options)

/*

 * Get chromosome sizes from a fasta file

 */

process GET_CHROM_SIZES {

    tag "$fasta"

    label 'process_low'

    publishDir "${params.outdir}",

        mode: params.publish_dir_mode,

        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:"genome", publish_id:'') }

    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)

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

        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"

    } else {

        container "quay.io/biocontainers/samtools:1.14--hb421002_0"

    }

    input:

    path fasta

    output:

    path '*.sizes'      , emit: sizes

    path '*.fai'        , emit: fai

    path  "versions.yml", emit: versions

    script:

    def software = 'samtools'

    """

    samtools faidx $fasta

    cut -f 1,2 ${fasta}.fai > ${fasta}.sizes

    cat <<-END_VERSIONS > versions.yml

    ${getProcessName(task.process)}:

        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

    END_VERSIONS

    """

}