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1 process GATHER_HITS {
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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}${params.fs}pigz${params.fs}2.7" : null)
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6 conda (params.enable_conda ? "conda-forge::pigz=2.6" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
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9 'quay.io/biocontainers/pigz:2.3.4' }"
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10
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11 input:
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12 tuple val(meta), path(genomes_fasta)
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13
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14 output:
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15 tuple val(meta), path("*_template_hits.txt"), emit: sm_template_hits
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def args2 = task.ext.args2 ?: ''
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24
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25 // Use input file ending as default
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26 prefix = task.ext.prefix ?: "${meta.id}"
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27 command = genomes_fasta.toString().endsWith('.gz') ? 'zcat' : 'cat'
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28 """
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29 $command \\
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30 $args \\
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31 $genomes_fasta | \\
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32 grep -F '>' | grep -E -o 'GC[AF]\\_[0-9]+\\.*[0-9]*' > ${prefix}.sm_template_hits.txt
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33
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34 cat <<-END_VERSIONS > versions.yml
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35 "${task.process}":
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36 pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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37 END_VERSIONS
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38
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39 mkdirver=""
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40 catver=""
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41 zver=""
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42 grepver=""
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43
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44 if [ "${workflow.containerEngine}" != "null" ]; then
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45 mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' )
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46 catver=\$( cat --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' )
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47 zver=\$( zcat --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
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48 grepver="\$mkdirver"
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49 else
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50 catver=\$( cat --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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51 zver=\$( zcat --version 2>&1 | sed '1!d; s/^.*(gzip) //' )
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52 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
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53 fi
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54
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55 cat <<-END_VERSIONS >> versions.yml
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56 cat: \$catver
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57 zcat: \$zver
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58 grep: \$grepver
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59 END_VERSIONS
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60 """
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61 } |
