--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/modules/mlst/main.nf	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,40 @@
+process MLST {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.23.0" : null)
+    conda (params.enable_conda ? "conda-forge::perl bioconda::mlst=2.23.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_1' :
+        'quay.io/biocontainers/mlst:2.23.0--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(fasta), path(datadir)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    when:
+    (task.ext.when == null || task.ext.when) && fasta.size() > 0
+
+    script:
+    def args = task.ext.args ?: ''
+    def taskid = (task.index ?: '')
+    def prefix = (meta.id ?: 'MLST' + taskid.toString())
+    def label = (params.mlst_label ? "--label '${prefix}'" : '')
+    args += (datadir ? " --datadir  '.' " : '')
+    """
+    mlst \\
+        --threads $task.cpus \\
+        $label \\
+        $args \\
+        $fasta > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
+    END_VERSIONS
+    """
+
+}
\ No newline at end of file