First version of complete M2 workflow

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2017, gatk-workflows
+Copyright (c) 2017, Broad Institute
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

generic.google-papi.options.json

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+{
+	"read_from_cache":false,
+	"default_runtime_attributes": {
+		"zones": "us-central1-a us-central1-b us-central1-c us-central1-f"
+	}
+}

mutect2.exome.inputs.json

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+{
+  "##_COMMENT1": "Runtime",
+  "Mutect2.gatk4_jar": "/root/gatk.jar",
+  "Mutect2.picard_jar": "gs://gatk-software/picard-2.10.0/picard.jar",
+  "Mutect2.m2_docker": "broadinstitute/gatk:4.beta.3",
+  "Mutect2.preemptible_attempts": 3,
+  "Mutect2.oncotator_docker": "broadinstitute/oncotator:1.9.3.0",
+
+  "##_COMMENT2": "Workflow options",
+  "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.artifact_modes": ["G/T", "C/T"],
+  "##_Mutect2.m2_extra_args": "(optional) String?",
+  "##_Mutect2.m2_extra_filtering_args": "(optional) String?",
+  "Mutect2.is_run_orientation_bias_filter": "True",
+  "Mutect2.is_run_oncotator": "True",
+
+  "##_COMMENT3": "Primary inputs",
+  "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",
+  "Mutect2.ref_fasta_index": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai",
+  "Mutect2.normal_bam": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bam",
+  "Mutect2.normal_bam_index": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bai",
+  "Mutect2.normal_sample_name": "HCC1143_BL",
+  "Mutect2.tumor_bam": "gs://gatk-best-practices/somatic-b37/HCC1143.bam",
+  "Mutect2.tumor_bam_index": "gs://gatk-best-practices/somatic-b37/HCC1143.bai",
+  "Mutect2.tumor_sample_name": "HCC1143",
+
+  "##_COMMENT4": "Primary resources",
+  "##_Mutect2.pon": "(optional) File?",
+  "##_Mutect2.pon_index": "(optional) File?",
+  "Mutect2.gnomad": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf",
+  "Mutect2.gnomad_index": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf.idx",
+  "Mutect2.variants_for_contamination": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf",
+  "Mutect2.variants_for_contamination_index": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf.idx",
+
+  "##_COMMENT5": "Secondary resources",
+  "Mutect2.onco_ds_tar_gz": "gs://gatk-best-practices/somatic-b37/oncotator_v1_ds_April052016.tar.gz",
+  "Mutect2.default_config_file": "gs://gatk-best-practices/somatic-b37/onco_config.txt",
+  "##_Mutect2.sequencing_center": "(optional) String?",
+  "##_Mutect2.sequence_source": "(optional) String?"
+}