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1 process BWA_IDX_MEM {
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2 tag "$meta.id"
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3 label 'process_micro'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}bwa${params.fs}0.7.17" : null)
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6 conda (params.enable_conda ? "bioconda::bwa=0.7.17 conda-forge::perl" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--he4a0461_11' :
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9 'quay.io/biocontainers/bwa:0.7.17--he4a0461_11' }"
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10
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11 input:
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12 tuple val(meta), path(genome), path(reads)
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13
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14 output:
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15 tuple val(meta), path("*.sam"), emit: aligned_sam
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def args2 = task.ext.args2 ?: ''
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24 def prefix = task.ext.prefix ?: "${meta.id}"
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25 """
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26
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27 bwa index $args $genome
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28 if [ "${params.fq_single_end}" = "false" ]; then
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29 bwa mem \\
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30 $args2 \\
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31 -t $task.cpus \\
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32 -a $genome \\
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33 ${reads[0]} > ${prefix}.aligned_1.sam
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34 bwa mem \\
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35 $args2 \\
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36 -t $task.cpus \\
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37 -a $genome \\
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38 ${reads[1]} > ${prefix}.aligned_2.sam
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39 else
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40 bwa mem \\
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41 $args2 \\
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42 -t $task.cpus \\
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43 -a $genome \\
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44 $reads > ${prefix}.aligned.sam
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45
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46 fi
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47
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48 cat <<-END_VERSIONS > versions.yml
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49 "${task.process}":
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50 bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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51 END_VERSIONS
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52 """
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53 } |
