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0
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1 process CAT_UNIQUE {
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2 tag "${meta.id}"
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3 label "process_pico"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
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6 conda (params.enable_conda ? "conda-forge::perl conda-forge::coreutils bioconda::perl-bioperl=1.7.8" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
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9 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
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10
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11 input:
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12 tuple val(meta), path(file)
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13
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14 output:
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15 path '*_uniq.txt' , emit: txt
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16 path '*metadata.csv', emit: csv, optional: true
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17 path 'versions.yml' , emit: versions
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18
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19 when:
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20 task.ext.when == null || task.ext.when
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21
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22 script:
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23 def args = (task.ext.args ?: '')
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24 def skip = (meta.skip_header ?: 1)
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25 prefix = (task.ext.prefix ?: meta.id)
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26 """
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27 newfile=\$(echo "$file" | sed -e 's/_w_dups/_uniq/g')
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28
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29 head -n$skip "$file" > \$newfile
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30 tail -n+\$(($skip + 1)) "$file" | sort -n | uniq >> \$newfile
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31
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32 if [ "\$newfile" == "iTOL_metadata_uniq.txt" ]; then
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33 head -n3 "$file" | tail -n1 | sed -e 's/^FIELD_LABELS/ID/' > microreact_metadata.csv
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34 tail -n+\$(($skip + 1)) "$file" | sort -n | uniq >> microreact_metadata.csv
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35 fi
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36
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37 uniqver=""
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38
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39 if [ "${workflow.containerEngine}" != "null" ]; then
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40 uniqver=\$( uniq --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
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41
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42 else
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43 uniqver=\$( uniq --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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44 fi
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45
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46 cat <<-END_VERSIONS > versions.yml
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47 "${task.process}":
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48 head: \$uniqver
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49 tail: \$uniqver
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50 sort: \$uniqver
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51 uniq: \$uniqver
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52 END_VERSIONS
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53 """
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54 } |
