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1 process ABRICATE_SUMMARY {
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2 tag "${abdbs.join(',')}"
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3 label 'process_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}abricate${params.fs}1.0.1" : null)
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6 conda (params.enable_conda ? "bioconda::abricate=1.0.1 conda-forge::coreutils" : 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/abricate%3A1.0.1--ha8f3691_1':
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9 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
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10
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11 input:
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12 tuple val(abdbs), path(abfiles)
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13
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14 output:
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15 tuple val('abricate_ncbi'), path("*.ncbi.absum.txt") , emit: ncbi, optional: true
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16 tuple val('abricate_ncbiamrplus'), path("*.ncbiamrplus.absum.txt"), emit: ncbiamrplus, optional: true
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17 tuple val('abricate_resfinder'), path("*resfinder.absum.txt") , emit: resfinder, optional: true
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18 tuple val('abricate_megares'), path("*.megares.absum.txt") , emit: megares, optional: true
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19 tuple val('abricate_argannot'), path("*.argannot.absum.txt") , emit: argannot, optional: true
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20 tuple val('abricate_ecoli_vf'), path("*.ecoli_vf.absum.txt") , emit: ecoli_vf, optional: true
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21 path "versions.yml" , emit: versions
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22
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23 when:
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24 task.ext.when == null || task.ext.when
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25
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26 script:
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27 def args = task.ext.args ?: ''
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28 def onthese = abdbs.collect{ db ->
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29 abfiles.findAll { files ->
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30 files =~ /\.${db}/
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31 }.join(' ')
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32 }.join('\\n')
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33 """
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34 filenum="1"
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35
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36 echo -e "$onthese" | while read -r files; do
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37 db=\$( echo -e "\${files}" | grep -E -o '\\w+\\.ab\\.txt' | sort -u | sed -e 's/.ab.txt//' )
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38
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39 if [ -z "\$db" ]; then
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40 db="\$filenum"
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41 fi
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42
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43 abricate \\
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44 $args \\
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45 --summary \${files} \\
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46 1> "abricate.\${db}.absum.txt"
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47
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48 sed -i -e "s/.\${db}.ab.txt//" "abricate.\${db}.absum.txt"
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49 sed -i -e 's/.assembly_filtered_contigs.fasta//' "abricate.\${db}.absum.txt"
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50
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51 filenum=\$((filenum+1))
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52 done
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53
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54 cat <<-END_VERSIONS > versions.yml
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55 "${task.process}":
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56 abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
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57 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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58 END_VERSIONS
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59
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60 sedver=""
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61 sortver=""
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62 grepver=""
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63
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64 if [ "${workflow.containerEngine}" != "null" ]; then
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65 sortver=\$( sort --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
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66 sedver="\$sortver"
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67 grepver="\$sortver"
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68 else
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69 sortver=\$( sort --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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70 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
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71 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
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72 fi
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73
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74 cat <<-END_VERSIONS >> versions.yml
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75 sort: \$sortver
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76 grep: \$grepver
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77 sed: \$sedver
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78 END_VERSIONS
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79 """
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80 } |
