--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.6.1/modules/megahit/assemble/main.nf	Tue Sep 05 11:51:40 2023 -0400
@@ -0,0 +1,57 @@
+process MEGAHIT_ASSEMBLE {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}megahit${params.fs}1.2.9" : null)
+    conda (params.enable_conda ? "conda-forge::python bioconda::megahit=1.2.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h2e03b76_1' :
+        'quay.io/biocontainers/megahit:1.2.9--h2e03b76_1' }"
+
+    input:
+        tuple val(meta), path(reads)
+
+    output:
+        tuple val(meta), path("${meta.id}${params.fs}${meta.id}.contigs.fa"), emit: assembly, 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 maxmem = task.memory ? "--memory ${task.memory.toBytes()}" : ""
+        if (meta.single_end) {
+            """
+            megahit \\
+                -r ${reads} \\
+                -t $task.cpus \\
+                $maxmem \\
+                $args \\
+                --out-dir $prefix \\
+                --out-prefix $prefix
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
+            END_VERSIONS
+            """
+        } else {
+            """
+            megahit \\
+                -1 ${reads[0]} \\
+                -2 ${reads[1]} \\
+                -t $task.cpus \\
+                $maxmem \\
+                $args \\
+                --out-dir $prefix \\
+                --out-prefix $prefix
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
+            END_VERSIONS
+            """
+    }
+}