From efd6394d829b6740d3dc5df0dc0483662ad753d9 Mon Sep 17 00:00:00 2001 From: David Benjamin Date: Wed, 17 Aug 2022 17:25:11 -0400 Subject: [PATCH] whoops, more fixing json --- scripts/m2_cromwell_tests/mutect2.inputs.json | 4 ---- scripts/m2_cromwell_tests/test_m2_wdl.json | 3 +-- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/scripts/m2_cromwell_tests/mutect2.inputs.json b/scripts/m2_cromwell_tests/mutect2.inputs.json index 4c7a08074eb..e67ed3c7356 100644 --- 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 index e8f85f4bbdc..259bb43ae45 100644 --- 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 } \ No newline at end of file