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1 process KMA_ALIGN {
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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}${params.fs}kma${params.fs}1.4.4" : null)
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6 conda (params.enable_conda ? "conda-forge::libgcc-ng bioconda::kma=1.4.3" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/kma:1.4.3--h7132678_1':
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9 'quay.io/biocontainers/kma:1.4.3--h7132678_1' }"
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10
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11 input:
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12 tuple val(meta), path(reads), path(index)
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13
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14 output:
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15 path "${meta.id}_kma_res"
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16 tuple val(meta), path("${meta.id}_kma_res${params.fs}*.res") , emit: res
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17 tuple val(meta), path("${meta.id}_kma_res${params.fs}*.mapstat") , emit: mapstat, optional: true
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18 tuple val(meta), path("${meta.id}_kma_res${params.fs}*.frag.gz") , emit: frags, optional: true
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19 tuple val(meta), path("${meta.id}_kma_res${params.fs}*_template_hits.txt"), emit: hits, optional: true
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20 path "versions.yml" , emit: versions
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21
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22 when:
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23 task.ext.when == null || task.ext.when
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24
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25 script:
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26 def args = task.ext.args ?: ''
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27 def prefix = task.ext.prefix ?: "${meta.id}"
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28 def reads_in = (meta.single_end ? "-i $reads" : "-ipe ${reads[0]} ${reads[1]}")
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29 def db = (meta.kma_t_db ?: "${index}")
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30 def db_basename = (db ? "${index.baseName}" : '')
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31 def get_hit_accs = (meta.get_kma_hit_accs ? 'true' : 'false')
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32 def res_dir = prefix + '_kma_res'
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33 reads_in = (params.kmaalign_int ? "-int $reads" : "-i $reads")
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34 """
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35 mkdir -p $res_dir || exit 1
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36 kma \\
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37 $args \\
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38 -t_db $db${params.fs}$db_basename \\
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39 -t $task.cpus \\
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40 -o $res_dir${params.fs}$prefix \\
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41 $reads_in
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42
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43 if [ "$get_hit_accs" == "true" ]; then
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44 grep -v '^#' $res_dir${params.fs}${prefix}.res | \\
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45 grep -E -o 'GC[AF]\\_[0-9]+\\.*[0-9]*' > $res_dir${params.fs}${prefix}_template_hits.txt
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46 fi
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47
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48 cat <<-END_VERSIONS > versions.yml
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49 "${task.process}":
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50 kma: \$( kma -v | sed -e 's%KMA-%%' )
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51 END_VERSIONS
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52
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53 mkdirver=""
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54 cutver=""
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55 grepver=""
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56
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57 if [ "${workflow.containerEngine}" != "null" ]; then
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58 mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' )
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59 cutver="\$mkdirver"
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60 grepver="\$mkdirver"
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61 else
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62 mkdirver=\$( mkdir --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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63 cutver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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64 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
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65 fi
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66
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67 cat <<-END_VERSIONS >> versions.yml
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68 mkdir: \$mkdirver
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69 cut: \$cutver
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70 grep: \$grepver
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71 END_VERSIONS
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72 """
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73 } |
