From 9718dedcfe396a8b6689260a37d13a5c4ec9a306 Mon Sep 17 00:00:00 2001
From: Pablo Riesgo Ferreiro <priesgoferreiro@gmail.com>
Date: Mon, 25 Apr 2022 10:20:42 +0200
Subject: [PATCH] ensures the GATK sort before mark duplicates uses the right
 tmp folder

---
 README.md                     | 2 +-
 modules/02_mark_duplicates.nf | 1 +
 nextflow.config               | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index d47d034..f8ab03f 100644
--- a/README.md
+++ b/README.md
@@ -142,7 +142,7 @@ This issue is described here and the solution is to use Java 8 https://gatk.broa
 
 
 
-## Biblipgraphy
+## Bibliography
 
 * DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, Kernytsky A, Sivachenko A, Cibulskis K, Gabriel S, Altshuler D, Daly M. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet, 43:491-498. DOI: 10.1038/ng.806.
 * Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. 10.1038/nbt.3820
diff --git a/modules/02_mark_duplicates.nf b/modules/02_mark_duplicates.nf
index 5b628d6..3e4307f 100644
--- a/modules/02_mark_duplicates.nf
+++ b/modules/02_mark_duplicates.nf
@@ -29,6 +29,7 @@ process MARK_DUPLICATES {
     mkdir tmp
 
     gatk SortSam \
+    --java-options '-Xmx${params.mark_duplicates_memory}  -Djava.io.tmpdir=./tmp' \
     --INPUT ${bam} \
     --OUTPUT ${name}.sorted.bam \
     --SORT_ORDER coordinate
diff --git a/nextflow.config b/nextflow.config
index f0e2d47..5573d6f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -44,7 +44,7 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 cleanup = true
 
-VERSION = '1.9.0'
+VERSION = '1.9.1'
 DOI = 'https://zenodo.org/badge/latestdoi/358400957'
 
 manifest {