Clean m2 wdl. Closes #4072. (#4132)

broadinstitute · Jan 14, 2018 · b4d1ddd · b4d1ddd
1 parent 186e6ef
commit b4d1ddd
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Showing 13 changed files with 1,090 additions and 1,041 deletions.
diff --git a/scripts/m2_cromwell_tests/test_m2_wdl_multi.json b/scripts/m2_cromwell_tests/test_m2_wdl_multi.json
@@ -1,19 +1,18 @@
 {
-  "Mutect2_Multi.gatk4_jar": "/root/gatk.jar",
+  "Mutect2_Multi.picard": "/home/travis/picard.jar",
+  "Mutect2_Multi.gatk_docker": "__GATK_DOCKER__",
+  "Mutect2_Multi.oncotator_docker": "broadinstitute/oncotator:1.9.6.1",
   "Mutect2_Multi.intervals": "/home/travis/build/broadinstitute/gatk/scripts/m2_cromwell_tests/interval_list.interval_list",
   "Mutect2_Multi.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta",
-  "Mutect2_Multi.ref_fasta_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai",
+  "Mutect2_Multi.ref_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai",
   "Mutect2_Multi.ref_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.dict",
   "Mutect2_Multi.pair_list": "/home/travis/build/broadinstitute/gatk/scripts/m2_cromwell_tests/pair_list",
   "Mutect2_Multi.scatter_count": 2,
   "Mutect2_Multi.dbsnp": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/dbsnp_138.b37.20.21.vcf",
   "Mutect2_Multi.dbsnp_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/dbsnp_138.b37.20.21.vcf.idx",
   "Mutect2_Multi.is_run_orientation_bias_filter": true,
   "Mutect2_Multi.is_run_oncotator": true,
-  "Mutect2_Multi.gatk_docker": "__GATK_DOCKER__",
-  "Mutect2_Multi.oncotator_docker": "broadinstitute/oncotator:1.9.3.0",
   "Mutect2_Multi.preemptible_attempts": 2,
   "Mutect2_Multi.artifact_modes": ["G/T", "C/T"],
-  "Mutect2_Multi.picard_jar": "/home/travis/picard.jar",
   "Mutect2_Multi.onco_ds_local_db_dir": "/root/"
 }