--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/modules/pirate/main.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,39 @@
+process PIRATE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}pirate${params.fs}5.2.0" : null)
+    conda (params.enable_conda ? "bioconda::pirate=1.0.5 bioconda::mcl=14.137 conda-forge::r-dplyr" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pirate:1.0.5--hdfd78af_0' :
+        'quay.io/biocontainers/pirate:1.0.5--hdfd78af_0' }"
+
+    input:
+        tuple val(meta), path(gff)
+
+    output:
+        tuple val(meta), path("results/*")                   , emit: results
+        tuple val(meta), path("results/core_alignment.fasta"), emit: aln, optional: true
+        path "versions.yml"                                  , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        def rplots = (params.enable_conda ? '--rplots' : '')
+        """
+        PIRATE \\
+            $args \\
+            $rplots \\
+            --threads $task.cpus \\
+            --input ".${params.fs}" \\
+            --output results/
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
+        END_VERSIONS
+        """
+}
\ No newline at end of file