nf_modules: add picard

src/nf_modules/picard/main.nf

+version = "2.18.11"
+container_url = "lbmc/picard:${version}"
+
+process mark_duplicate {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  publishDir "results/mapping/ddup/", mode: 'copy'
+
+  input:
+    tuple val(file_id), path(bam)
+  output:
+    tuple val(file_id) , path("*.bam"), emit: bam
+    path "*_report.txt", emit: report
+
+
+  script:
+"""
+PicardCommandLine MarkDuplicates \
+  VALIDATION_STRINGENCY=LENIENT \
+  REMOVE_DUPLICATES=true \
+  INPUT=${bams[0]} \
+  OUTPUT=${bams[0].baseName}_dedup.bam \
+  METRICS_FILE=${bams[0].baseName}_picard_dedup_report.txt &> \
+  picard_${bams[0].baseName}.log
+"""
+}