From a3d3e95b15d8850d6af81b92bebbdb46f78dee2b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 22 Jan 2021 14:56:17 +0100
Subject: [PATCH] nf_modules: add picard
---
src/nf_modules/picard/main.nf | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
create mode 100644 src/nf_modules/picard/main.nf
diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf
new file mode 100644
index 00000000..47ba54b6
--- /dev/null
+++ b/src/nf_modules/picard/main.nf
@@ -0,0 +1,27 @@
+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
+"""
+}
--
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