--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/modules/polypolish/main.nf	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,36 @@
+process POLYPOLISH {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}polypolish${params.fs}0.5.0" : null)
+    conda (params.enable_conda ? "bioconda::polypolish=0.5.0 conda-forge::libgcc-ng" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/polypolish:0.5.0--hdbdd923_4' :
+        'quay.io/biocontainers/polypolish:0.5.0--hdbdd923_4' }"
+
+    input:
+        tuple val(meta), path(genome), path(sam)
+
+    output:
+        tuple val(meta), path("*.polished.fa"), emit: polished
+        path  "versions.yml"                  , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args   = task.ext.args ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        """
+
+        polypolish \\
+            $args \\
+            $genome \\
+            ${sam.join(' ')} > ${prefix}.polished.fa
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            polypolish: \$(echo \$(polypolish -V 2>&1) | sed 's/^Polypolish v//')
+        END_VERSIONS
+        """
+}
\ No newline at end of file