From 196c4585d2e9f1f962d09cefcf11e36659c6598c Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Mon, 1 Aug 2016 22:47:13 -0400 Subject: [PATCH] Update bucket filepaths in gotc json --- .../PublicPairedSingleSampleWf_160720.inputs.json | 59 ++++++++++++++++++++-- 1 file changed, 55 insertions(+), 4 deletions(-) diff --git a/scripts/broad_pipelines/PublicPairedSingleSampleWf_160720.inputs.json b/scripts/broad_pipelines/PublicPairedSingleSampleWf_160720.inputs.json index 0f5f756..65b3a4f 100644 --- a/scripts/broad_pipelines/PublicPairedSingleSampleWf_160720.inputs.json +++ b/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",