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 {