--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/bbtools/bbmerge/main.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,44 @@
+process BBTOOLS_BBMERGE {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}bbtools${params.fs}38.94" : null)
+    conda (params.enable_conda ? "conda-forge::pbzip2 bioconda::bbmap=38.95" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bbmap:38.95--he522d1c_0' :
+        'quay.io/biocontainers/bbmap:38.95--he522d1c_0' }"
+
+    input:
+        tuple val(meta), path(reads)
+
+    output:
+        tuple val(meta), path("*.fastq.gz"), emit: fastq
+        tuple val(meta), path("*.log")     , emit: log
+        path "versions.yml"                , emit: versions
+
+    when:
+        !meta.single_end
+
+    script:
+        def args = task.ext.args ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        def in_files = "in1=${reads[0]} in2=${reads[1]}"
+        def out_file  = "out=${prefix}.bbmerge.fastq.gz"
+        def adapters_file = file (meta.adapters)
+        def adapters = !("${adapters_file.simpleName}" ==~ 'dummy_file.*') && adapters_file.exits() ? "adapters=${meta.adapters}" : ''
+        def args_formatted = args.replaceAll('=\s+', '=')
+        """
+        bbmerge.sh \\
+            -Xmx${task.memory.toGiga()}G \\
+            threads=$task.cpus \\
+            $args_formatted \\
+            $adapters \\
+            $in_files \\
+            $out_file &> ${prefix}.bbmerge.log
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            bbmerge: \$( bbversion.sh )
+        END_VERSIONS
+        """
+}