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updated command lines for WDL tests for C29
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@samuelklee
samuelklee committed Dec 29, 2017
1 parent b1b0909 commit 63f9f8a
Showing 1 changed file with 8 additions and 8 deletions.
16 changes: 8 additions & 8 deletions scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
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Expand Up @@ -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 ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl cnv_germline_case_wgs_do-gc_workflow_mod.json
java -jar ~/${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

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