whoops, more fixing json

broadinstitute · Aug 17, 2022 · efd6394 · efd6394
1 parent 14e2504
commit efd6394
Show file tree

Hide file tree

Showing 2 changed files with 1 addition and 6 deletions.
diff --git a/scripts/m2_cromwell_tests/mutect2.inputs.json b/scripts/m2_cromwell_tests/mutect2.inputs.json
@@ -4,10 +4,6 @@
   "Mutect2.intervals": "gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list",
   "Mutect2.scatter_count": 50,
   "Mutect2.m2_extra_args": "--downsampling-stride 20 --max-reads-per-alignment-start 6 --max-suspicious-reads-per-alignment-start 6",
-  "Mutect2.filter_funcotations": "True",
-  "Mutect2.funco_reference_version": "hg19",
-  "Mutect2.funco_data_sources_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz",
-  "Mutect2.funco_transcript_selection_list": "gs://broad-public-datasets/funcotator/transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt",
 
   "Mutect2.ref_fasta": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta",
   "Mutect2.ref_dict": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict",

diff --git a/scripts/m2_cromwell_tests/test_m2_wdl.json b/scripts/m2_cromwell_tests/test_m2_wdl.json
@@ -10,8 +10,7 @@
   "Mutect2.normal_reads_index": "/home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam.bai",
   "Mutect2.scatter_count": 2,
   "Mutect2.run_orientation_bias_mixture_model_filter": true,
-  "Mutect2.run_funcotator": true,
-  "Mutect2.preemptible_attempts": 2,
+  "Mutect2.preemptible": 2,
   "Mutect2.compress_vcfs": false,
   "Mutect2.make_bamout": true
 }