nf_modules: add samtools DSL2

src/nf_modules/samtools/main.nf

+version = "1.17"
+container_url = "lbmc/samtools:${version}"
+
+process filter_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+    path bed
+
+  output:
+    tuple val(file_id), path("*_filtered.bam"), emit: bam
+  script:
+"""
+samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${file_id}_filtered.bam
+"""
+}
+
+process index_bam {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+
+  script:
+"""
+samtools index ${bam}
+"""
+}
+
+process sort_bam {
+  container = "${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:
+"""
+samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${bam}
+"""
+}
+
+
+process split_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  cpus = 2
+
+  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:
+"""
+samtools view -hb -F 0x10 ${bam} > ${file_id}_forward.bam &
+samtools view -hb -f 0x10 ${bam} > ${file_id}_reverse.bam
+"""
+}
+
+
+process merge_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  cpus = 2
+
+  input:
+    tuple val(first_file_id), path(first_bam)
+    tuple val(second_file_id), path(second_bam)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+  script:
+"""
+samtools merge ${first_bam} ${second_bam} ${first_bam_id}_${second_file_id}.bam
+"""
+}