nf_modules: add sambamba to DSL2

src/nf_modules/sambamba/main.nf

+version = "0.6.7"
+container_url = "lbmc/sambamba:${version}"
+
+process index_bam {
+  container = "${container_url}"
+  label "big_mem__cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+
+  script:
+"""
+sambamba index -t ${task.cpus} ${bam}
+"""
+}
+
+process sort_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+
+  script:
+"""
+sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
+"""
+}
+
+
+process split_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*_forward.bam*"), emit: bam_forward
+    tuple val(file_id), path("*_reverse.bam*"), emit: bam_reverse
+  script:
+"""
+sambamba view -t ${task.cpus} -h -F "strand == '+'" ${bam} > ${file_id}_forward.bam
+sambamba view -t ${task.cpus} -h -F "strand == '-'" ${bam} > ${file_id}_reverse.bam
+"""
+}