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1 process BWA_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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--he4a0461_11' :
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9 'quay.io/biocontainers/bwa:0.7.17--he4a0461_11' }"
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10
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11 input:
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12 tuple val(meta), path(reads), path(index)
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13 val index2
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14
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15 output:
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16 tuple val(meta), path("*.sam"), emit: aligned_sam
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 def args2 = task.ext.args2 ?: ''
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25 def prefix = task.ext.prefix ?: "${meta.id}"
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26 def this_index = (index ?: index2)
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27 """
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28
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29 if [ "${params.fq_single_end}" = "false" ]; then
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30 bwa mem \\
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31 $args \\
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32 -t $task.cpus \\
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33 $this_index \\
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34 ${reads[0]} ${reads[1]} > ${prefix}.aligned.sam
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35 else
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36 bwa mem \\
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37 $args \\
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38 -t $task.cpus \\
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39 -a \\
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40 $this_index \\
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41 $reads > ${prefix}.aligned.sam
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42
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43 fi
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44
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45 cat <<-END_VERSIONS > versions.yml
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46 "${task.process}":
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47 bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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48 END_VERSIONS
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49 """
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50 } |
