Merge pull request #8 from TRON-Bioinformatics/tmp-folder-strikes-back

ensures the GATK sort before mark duplicates uses the right tmp folder

Author: priesgo

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

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

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 {