Mercurial > repos > dvanzessen > bcbio_nextgen_emc

changeset 4:7211d3a78fe0 draft

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Uploaded
author dvanzessen
date Fri, 26 Jul 2019 03:54:39 -0400
parents cb60ea3f8f62
children 00c95e2d8820
files bcbio-nextgen.xml
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/bcbio-nextgen.xml	Mon Jul 22 04:59:16 2019 -0400
+++ b/bcbio-nextgen.xml	Fri Jul 26 03:54:39 2019 -0400
@@ -10,7 +10,7 @@
         #for $i, $sample in enumerate( $samples )
             --input $sample.forward:$sample.reverse:$sample.phenotype
         #end for
-        && bcbio_nextgen.py \$BCBIO_DIRECTORY/galaxy/bcbio_system.yaml `pwd`/config.yaml && 
+        && bcbio_nextgen.py \$BCBIO_DIRECTORY/galaxy/bcbio_system.yaml `pwd`/config.yaml -t local -n \$BCBIO_CORES && 
         zcat final/*/Batch1-ensemble-annotated.vcf.gz > $output_vcf &&
         python $__tool_directory__/make_html.py --input-dir $everything_else.files_path --root-html $everything_else
     ]]></command>