From 63f9f8a04eb4811d24ff75d7e175023bcc03e410 Mon Sep 17 00:00:00 2001 From: Samuel Lee Date: Thu, 28 Dec 2017 14:56:27 -0500 Subject: [PATCH] updated command lines for WDL tests for C29 --- .../germline/run_cnv_germline_workflows.sh | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh index 3981ad27ea5..9c9c5c83e87 100644 --- a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh +++ b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh @@ -40,19 +40,19 @@ CROMWELL_JAR="cromwell-0.29.jar" # We disable some tests to reduce runtime on Travis # Cohort WES -java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl cnv_germline_cohort_wes_no-gc_workflow_mod.json +java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_wes_no-gc_workflow_mod.json # Cohort WGS -#java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl cnv_germline_cohort_wgs_no-gc_workflow_mod.json +#java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_wgs_no-gc_workflow_mod.json # Cohort WES w/ explicit GC correction -java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl cnv_germline_cohort_wes_do-gc_workflow_mod.json +java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_wes_do-gc_workflow_mod.json # Cohort WGS w/ explicit GC correction -#java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl cnv_germline_cohort_wgs_do-gc_workflow_mod.json +#java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_wgs_do-gc_workflow_mod.json # Case WES -java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl cnv_germline_case_wes_no-gc_workflow_mod.json +java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl -i cnv_germline_case_wes_no-gc_workflow_mod.json # Case WGS -#java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl cnv_germline_case_wgs_no-gc_workflow_mod.json +#java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl -i cnv_germline_case_wgs_no-gc_workflow_mod.json # Case WES w/ explicit GC correction -#java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl cnv_germline_case_wes_do-gc_workflow_mod.json +#java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl -i cnv_germline_case_wes_do-gc_workflow_mod.json # Case WGS w/ explicit GC correction -java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl cnv_germline_case_wgs_do-gc_workflow_mod.json \ No newline at end of file +java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl -i cnv_germline_case_wgs_do-gc_workflow_mod.json \ No newline at end of file