--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/modules/masurca/polish/main.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,42 @@
+process MASURCA_POLISH {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}masurca${params.fs}4.1.0" : null)
+    conda (params.enable_conda ? "bioconda::masurca=4.1.0 conda-forge::libgcc-ng" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/masurca:4.1.0--pl5321hb5bd705_1' :
+        'quay.io/biocontainers/masurca:4.1.0--pl5321hb5bd705_1' }"
+
+    input:
+        tuple val(meta), path(contigs), path(reads)
+
+    output:
+        tuple val(meta), path("${prefix}_contigs.fa"), emit: polished
+        path "versions.yml"                          , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args           = task.ext.args ?: ''
+        def memory         = task.memory.toGiga()
+        def mem_per_thread = task.memory.toGiga().toInteger().div(task.cpus.toInteger()).round(0)
+        def all_reads      = "${reads.join(' ')}"
+        prefix             = (task.ext.prefix ?: meta.id)
+        """
+        polca.sh \\
+            -a $contigs \\
+            -r '${all_reads}' \\
+            -t $task.cpus \\
+            -m $mem_per_thread \\
+            $args \\
+        
+        mv 'contigs.fa' "${prefix}.contigs.fa"
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            masurca: \$(echo \$(masurca --version 2>&1) | sed 's/^.*version //')
+        END_VERSIONS
+    """
+}
\ No newline at end of file