Revert bt2 update

process BOWTIE2_ALIGN {

    tag "$meta.id"

    label "process_high"

    label 'process_high'

    conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)

    container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?

        "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :

        "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"

    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :

        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"

    input:

    tuple val(meta), path(reads)

    path  index

    val   save_unaligned

    val   sort_bam

    output:

    tuple val(meta), path("*.bam")    , emit: bam

    tuple val(meta), path("*.log")    , emit: log

    tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true

    tuple val(meta), path('*.bam')    , emit: bam

    tuple val(meta), path('*.log')    , emit: log

    tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true

    path  "versions.yml"              , emit: versions

    when:

    task.ext.when == null || task.ext.when

    script:

    def args = task.ext.args ?: ""

    def args2 = task.ext.args2 ?: ""

    def args = task.ext.args ?: ''

    def args2 = task.ext.args2 ?: ''

    def prefix = task.ext.prefix ?: "${meta.id}"

    def unaligned = ""

    def reads_args = ""

    if (meta.single_end) {

        unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""

        reads_args = "-U ${reads}"

    } else {

        unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""

        reads_args = "-1 ${reads[0]} -2 ${reads[1]}"

    }

    def samtools_command = sort_bam ? 'sort' : 'view'

        def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''

        """

    INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`

    [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`

    [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1

        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`

        [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`

        [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1

        bowtie2 \\

            -x \$INDEX \\

            -U $reads \\

            --threads $task.cpus \\

            $unaligned \\

            $args \\

            2> ${prefix}.bowtie2.log \\

            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -

        cat <<-END_VERSIONS > versions.yml

        "${task.process}":

            bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')

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

            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )

        END_VERSIONS

        """

    } else {

        def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''

        """

        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`

        [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`

        [ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1

        bowtie2 \\

            -x \$INDEX \\

        $reads_args \\

            -1 ${reads[0]} \\

            -2 ${reads[1]} \\

            --threads $task.cpus \\

            $unaligned \\

            $args \\

            2> ${prefix}.bowtie2.log \\

        | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -

            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -

        if [ -f ${prefix}.unmapped.fastq.1.gz ]; then

            mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz

        fi

        if [ -f ${prefix}.unmapped.fastq.2.gz ]; then

            mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz

        fi

        END_VERSIONS

        """

    }

}