--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/amrfinderplus/run/main.nf	Thu Jun 27 14:17:26 2024 -0400
@@ -0,0 +1,52 @@
+process AMRFINDERPLUS_RUN {
+    tag "$meta.id"
+    label 'process_low'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}amrfinderplus${params.fs}3.10.24" : null)
+    conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.24 conda-forge::libgcc-ng" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
+        'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("${prefix}.tsv")          , emit: report
+    tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true
+    path "versions.yml"                             , emit: versions
+
+    when:
+    (task.ext.when == null || task.ext.when) && fasta.size() > 0
+
+    script:
+    def args = task.ext.args ?: ''
+    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
+    prefix = task.ext.prefix ?: "${meta.id}"
+    organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
+    fasta_name = fasta.getName().replace(".gz", "")
+    fasta_param = "-n"
+    if (meta.containsKey("is_proteins")) {
+        if (meta.is_proteins) {
+            fasta_param = "-p"
+        }
+    }
+    """
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    amrfinder \\
+        $fasta_param $fasta_name \\
+        $organism_param \\
+        $args \\
+        --threads $task.cpus > ${prefix}.tsv
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        amrfinderplus: \$(amrfinder --version)
+        gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' )
+    END_VERSIONS
+    """
+}
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