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1 process AMRFINDERPLUS_RUN {
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2 tag "$meta.id"
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3 label 'process_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}amrfinderplus${params.fs}3.10.24" : null)
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6 conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.24 conda-forge::libgcc-ng" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
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9 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
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10
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11 input:
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12 tuple val(meta), path(fasta)
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13
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14 output:
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15 tuple val(meta), path("${prefix}.tsv") , emit: report
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16 tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20 (task.ext.when == null || task.ext.when) && fasta.size() > 0
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 def is_compressed = fasta.getName().endsWith(".gz") ? true : false
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25 prefix = task.ext.prefix ?: "${meta.id}"
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26 organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
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27 fasta_name = fasta.getName().replace(".gz", "")
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28 fasta_param = "-n"
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29 if (meta.containsKey("is_proteins")) {
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30 if (meta.is_proteins) {
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31 fasta_param = "-p"
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32 }
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33 }
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34 """
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35 if [ "$is_compressed" == "true" ]; then
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36 gzip -c -d $fasta > $fasta_name
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37 fi
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38
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39 amrfinder \\
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40 $fasta_param $fasta_name \\
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41 $organism_param \\
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42 $args \\
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43 --threads $task.cpus > ${prefix}.tsv
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44
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45
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46 cat <<-END_VERSIONS > versions.yml
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47 "${task.process}":
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48 amrfinderplus: \$(amrfinder --version)
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49 gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' )
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50 END_VERSIONS
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51 """
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52 } |
