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1 process CENTRIFUGE_EXTRACT {
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2 tag "$meta.id"
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3 label 'process_low'
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4
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5 //seqkit container contains required bash and other utilities
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6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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7 conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::coreutils" : null)
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8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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9 'https://depot.galaxyproject.org/singularity/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0':
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10 'quay.io/biocontainers/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0' }"
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11
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12 input:
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13 tuple val(meta), path(centrifuge_report)
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14 tuple val(meta), path(centrifuge_output)
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15
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16 output:
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17 tuple val(meta), path('*.extract-centrifuge-bug-ids.txt'), emit: extracted
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18 path "versions.yml" , emit: versions
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19
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20 when:
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21 task.ext.when == null || task.ext.when
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22
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23 script:
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24 def args = task.ext.args ?: ''
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25 def prefix = task.ext.prefix ?: "${meta.id}"
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26 """
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27 grep -F '${params.centrifuge_extract_bug}' $centrifuge_report \
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28 | cut -f2 \
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29 | sort -u \
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30 | while read -r taxId; do
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31 echo -e "\t\$taxId"'\$'
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32 done > gotcha.txt
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33
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34 cut -f1-3 $centrifuge_output | grep -E -f gotcha.txt | cut -f1 | sort -u > ${prefix}.extract-centrifuge-bug-ids.txt || true
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35
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36 cat <<-END_VERSIONS > versions.yml
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37 "${task.process}":
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38 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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39 END_VERSIONS
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40
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41 ver=""
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42 sedver=""
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43
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44 if [ "${workflow.containerEngine}" != "null" ]; then
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45 ver=\$( cut --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
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46 sedver="\$ver"
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47 else
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48 ver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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49 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
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50 fi
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51
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52 cat <<-END_VERSIONS >> versions.yml
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53 cut: \$ver
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54 tail: \$ver
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55 sort: \$ver
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56 sed: \$sedver
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57 END_VERSIONS
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58 """
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59 } |
