--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/modules/shovill/main.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,44 @@
+process SHOVILL {
+    tag "$meta.id"
+    label 'process_low'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}shovill${params.fs}1.1.0" : null)
+    conda (params.enable_conda ? "bioconda::shovill=1.1.0 conda-forge::pigz" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' :
+        'quay.io/biocontainers/shovill:1.1.0--0' }"
+
+    input:
+        tuple val(meta), path(reads)
+
+    output:
+        tuple val(meta), path("${prefix}${params.fs}contigs.fa")                         , emit: contigs
+        tuple val(meta), path("${prefix}${params.fs}shovill.corrections")                , emit: corrections
+        tuple val(meta), path("${prefix}${params.fs}shovill.log")                        , emit: log
+        tuple val(meta), path("${prefix}${params.fs}{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
+        tuple val(meta), path("${prefix}${params.fs}contigs.{fastg,gfa,LastGraph}")      , emit: gfa, optional: true
+        path "versions.yml"                                                              , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def memory = task.memory.toGiga()
+        prefix = (task.ext.prefix ?: meta.id)
+        """
+        shovill \\
+            --R1 ${reads[0]} \\
+            --R2 ${reads[1]} \\
+            $args \\
+            --cpus $task.cpus \\
+            --ram $memory \\
+            --outdir $prefix \\
+            --force
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            shovill: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
+        END_VERSIONS
+    """
+}
\ No newline at end of file