Merge pull request #48 from broadinstitute/gvda_update_gotc_json_buck…

…etpaths

Update bucket filepaths in gotc json

scripts/broad_pipelines/PublicPairedSingleSampleWf_160720.inputs.json

@@ -2,15 +2,66 @@
   "##_COMMENT1": "SAMPLE NAME AND UNMAPPED BAMS",
   "PairedEndSingleSampleWorkflow.sample_name": "NA12878",
   "PairedEndSingleSampleWorkflow.flowcell_unmapped_bams": [
-    "gs://genomics-public-data/test-data/dna/wgs/hiseqx/NA12878/H06HDADXX130110.1.ATCACGAT.20k_reads.bam",
-    "gs://genomics-public-data/test-data/dna/wgs/hiseqx/NA12878/H06HDADXX130110.2.ATCACGAT.20k_reads.bam",
-    "gs://genomics-public-data/test-data/dna/wgs/hiseqx/NA12878/H06JUADXX130110.1.ATCACGAT.20k_reads.bam"
+	"gs://genomics-public-data/test-data/dna/wgs/hiseq2500/NA12878/H06HDADXX130110.1.ATCACGAT.20k_reads.bam",
+	"gs://genomics-public-data/test-data/dna/wgs/hiseq2500/NA12878/H06HDADXX130110.2.ATCACGAT.20k_reads.bam",
+	"gs://genomics-public-data/test-data/dna/wgs/hiseq2500/NA12878/H06JUADXX130110.1.ATCACGAT.20k_reads.bam"
   ],
   "PairedEndSingleSampleWorkflow.final_gvcf_name": "NA12878.g.vcf.gz",
   "PairedEndSingleSampleWorkflow.unmapped_bam_suffix": ".bam",
   
   "##_COMMENT2": "INTERVALS",  
-  "PairedEndSingleSampleWorkflow.scattered_calling_intervals": ["gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0001_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0002_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0003_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0004_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0005_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0006_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0007_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0008_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0009_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0010_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0011_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0012_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0013_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0014_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0015_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0016_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0017_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0018_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0019_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0020_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0021_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0022_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0023_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0024_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0025_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0026_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0027_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0028_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0029_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0030_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0031_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0032_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0033_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0034_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0035_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0036_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0037_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0038_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0039_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0040_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0041_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0042_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0043_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0044_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0045_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0046_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0047_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0048_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0049_of_50/scattered.interval_list", "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0050_of_50/scattered.interval_list"],
+  "PairedEndSingleSampleWorkflow.scattered_calling_intervals": [
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0001_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0002_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0003_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0004_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0005_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0006_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0007_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0008_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0009_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0010_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0011_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0012_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0013_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0014_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0015_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0016_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0017_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0018_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0019_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0020_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0021_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0022_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0023_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0024_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0025_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0026_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0027_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0028_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0029_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0030_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0031_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0032_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0033_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0034_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0035_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0036_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0037_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0038_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0039_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0040_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0041_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0042_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0043_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0044_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0045_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0046_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0047_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0048_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0049_of_50/scattered.interval_list", 
+    "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0050_of_50/scattered.interval_list"
+  ],
   "PairedEndSingleSampleWorkflow.wgs_calling_interval_list": "gs://genomics-public-data/resources/broad/hg38/v0/wgs_calling_regions.hg38.interval_list",
   
   "##_COMMENT2": "OPTIONAL ARGUMENTS",