--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/bwa/mem/main.nf	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,50 @@
+process BWA_MEM {
+    tag "$meta.id"
+    label 'process_micro'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}bwa${params.fs}0.7.17" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 conda-forge::perl" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bwa:0.7.17--he4a0461_11' :
+        'quay.io/biocontainers/bwa:0.7.17--he4a0461_11' }"
+
+    input:
+        tuple val(meta), path(reads), path(index)
+        val index2
+
+    output:
+        tuple val(meta), path("*.sam"), emit: aligned_sam
+        path  "versions.yml"          , emit: versions
+
+    when:
+        
+
+    script:
+        def args   = task.ext.args ?: ''
+        def args2  = task.ext.args2 ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        def this_index = (index ?: index2)
+        """
+
+        if [ "${params.fq_single_end}" = "false" ]; then
+            bwa mem \\
+                $args \\
+                -t $task.cpus \\
+                $this_index \\
+                ${reads[0]} ${reads[1]} > ${prefix}.aligned.sam
+        else
+            bwa mem \\
+                $args \\
+                -t $task.cpus \\
+                -a \\
+                $this_index \\
+                $reads > ${prefix}.aligned.sam
+
+        fi
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
+        END_VERSIONS
+        """
+}
\ No newline at end of file