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Merge pull request #84 from HumanCellAtlas/ds_env_agnostic_inputs_539
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Use public inputs in example files
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David Shiga authored Feb 22, 2018
2 parents 5c9dd36 + 2ec3cfb commit 357e165
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Showing 4 changed files with 35 additions and 35 deletions.
30 changes: 15 additions & 15 deletions pipelines/optimus/example_test_inputs.json
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{
"Optimus.fastq_inputs": [
[
"gs://broad-dsde-mint-dev-teststorage/10x/demo/fastqs/pbmc8k_S1_L007_R1_001.fastq.gz",
"gs://broad-dsde-mint-dev-teststorage/10x/demo/fastqs/pbmc8k_S1_L007_R2_001.fastq.gz",
"gs://broad-dsde-mint-dev-teststorage/10x/demo/fastqs/pbmc8k_S1_L007_I1_001.fastq.gz"
],
[
"gs://broad-dsde-mint-dev-teststorage/10x/demo/fastqs/pbmc8k_S1_L007_R1_001.fastq.gz",
"gs://broad-dsde-mint-dev-teststorage/10x/demo/fastqs/pbmc8k_S1_L007_R2_001.fastq.gz",
"gs://broad-dsde-mint-dev-teststorage/10x/demo/fastqs/pbmc8k_S1_L007_I1_001.fastq.gz"
]
"Optimus.r1": [
"gs://hca-dcp-mint-test-data/10x/demo/fastqs/pbmc8k_S1_L007_R1_001.fastq.gz",
"gs://hca-dcp-mint-test-data/10x/demo/fastqs/pbmc8k_S1_L007_R1_001.fastq.gz"
],
"Optimus.whitelist": "gs://broad-dsde-mint-dev-teststorage/10x/whitelist/737K-august-2016.txt",
"Optimus.tar_star_reference": "gs://broad-dsde-mint-dev-teststorage/demo/star.tar",
"Optimus.r2": [
"gs://hca-dcp-mint-test-data/10x/demo/fastqs/pbmc8k_S1_L007_R2_001.fastq.gz",
"gs://hca-dcp-mint-test-data/10x/demo/fastqs/pbmc8k_S1_L007_R2_001.fastq.gz"
],
"Optimus.i1": [
"gs://hca-dcp-mint-test-data/10x/demo/fastqs/pbmc8k_S1_L007_I1_001.fastq.gz",
"gs://hca-dcp-mint-test-data/10x/demo/fastqs/pbmc8k_S1_L007_I1_001.fastq.gz"
],
"Optimus.whitelist": "gs://hca-dcp-mint-test-data/10x/whitelist/737K-august-2016.txt",
"Optimus.tar_star_reference": "gs://hca-dcp-mint-test-data/reference/demo/star.tar",
"Optimus.sample_id": "pbmc8k_test",
"Optimus.annotations_gtf": "gs://broad-dsde-mint-dev-teststorage/reference/hg19_ds/GSM1629193_hg19_ERCC.gtf.gz",
"Optimus.ref_genome_fasta": "gs://broad-dsde-mint-dev-teststorage/demo/chr21.fa"
"Optimus.annotations_gtf": "gs://hca-dcp-mint-test-data/reference/demo/hg19_ds/GSM1629193_hg19_ERCC.gtf.gz",
"Optimus.ref_genome_fasta": "gs://hca-dcp-mint-test-data/reference/demo/chr21.fa"
}
14 changes: 7 additions & 7 deletions pipelines/optimus/example_test_outputs.json
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"outputs": {
"Optimus.tag_gene_exon_log": [
[
"gs://broad-dsde-mint-dev-cromwell-execution/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-AlignTagCorrectUmis/shard-0/AlignTagCorrectUmis/d250b98d-a2f0-4b19-be86-e347bd076a5f/call-TagGeneExon/shard-0/gene_exon_tag_summary.log"
"gs://hca-dcp-mint-test-data/10x/demo/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-AlignTagCorrectUmis/shard-0/AlignTagCorrectUmis/d250b98d-a2f0-4b19-be86-e347bd076a5f/call-TagGeneExon/shard-0/gene_exon_tag_summary.log"
]
],
"Optimus.matrix_summary": "gs://broad-dsde-mint-dev-cromwell-execution/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-DropSeqToolsDigitalExpression/digital_expression_summary.txt",
"Optimus.matrix_summary": "gs://hca-dcp-mint-test-data/10x/demo/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-DropSeqToolsDigitalExpression/digital_expression_summary.txt",
"Optimus.umi_metrics": [
[
"gs://broad-dsde-mint-dev-cromwell-execution/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-AlignTagCorrectUmis/shard-0/AlignTagCorrectUmis/d250b98d-a2f0-4b19-be86-e347bd076a5f/call-CorrectUmiMarkDuplicates/shard-0/umi_metrics.txt"
"gs://hca-dcp-mint-test-data/10x/demo/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-AlignTagCorrectUmis/shard-0/AlignTagCorrectUmis/d250b98d-a2f0-4b19-be86-e347bd076a5f/call-CorrectUmiMarkDuplicates/shard-0/umi_metrics.txt"
]
],
"Optimus.duplicate_metrics": [
[
"gs://broad-dsde-mint-dev-cromwell-execution/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-AlignTagCorrectUmis/shard-0/AlignTagCorrectUmis/d250b98d-a2f0-4b19-be86-e347bd076a5f/call-CorrectUmiMarkDuplicates/shard-0/duplicate_metrics.txt"
"gs://hca-dcp-mint-test-data/10x/demo/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-AlignTagCorrectUmis/shard-0/AlignTagCorrectUmis/d250b98d-a2f0-4b19-be86-e347bd076a5f/call-CorrectUmiMarkDuplicates/shard-0/duplicate_metrics.txt"
]
],
"Optimus.matrix": "gs://broad-dsde-mint-dev-cromwell-execution/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-DropSeqToolsDigitalExpression/digital_expression.txt.gz",
"Optimus.bam": "gs://broad-dsde-mint-dev-cromwell-execution/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-MergeBam/out.bam",
"Optimus.picard_metrics": "gs://broad-dsde-mint-dev-cromwell-execution/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-CollectMultipleMetrics/pbmc8k_test.tar.gz"
"Optimus.matrix": "gs://hca-dcp-mint-test-data/10x/demo/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-DropSeqToolsDigitalExpression/digital_expression.txt.gz",
"Optimus.bam": "gs://hca-dcp-mint-test-data/10x/demo/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-MergeBam/out.bam",
"Optimus.picard_metrics": "gs://hca-dcp-mint-test-data/10x/demo/cromwell-executions/Optimus/c98322d7-406d-4e3f-96c8-e2bd1429e645/call-CollectMultipleMetrics/pbmc8k_test.tar.gz"
},
"id": "c98322d7-406d-4e3f-96c8-e2bd1429e645"
}
20 changes: 10 additions & 10 deletions pipelines/smartseq2_single_sample/ss2_single_sample_example.json
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{
"SmartSeq2SingleCell.gtf_file": "gs://broad-dsde-mint-dev-teststorage/reference/GRCh38_Gencode/gencode.v27.primary_assembly.annotation.gtf",
"SmartSeq2SingleCell.gtf_file": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode.v27.primary_assembly.annotation.gtf",
"SmartSeq2SingleCell.hisat2_ref_trans_name": "gencode_v27_trans_rsem",
"SmartSeq2SingleCell.rrna_intervals": "gs://broad-dsde-mint-dev-teststorage/reference/gencode.v27.rRNA.interval_list",
"SmartSeq2SingleCell.star_ref_index": "gs://broad-dsde-mint-dev-teststorage/reference/GRCh38_Gencode/GRCh38_GencodeV27_Primary.tar",
"SmartSeq2SingleCell.hisat2_ref_index": "gs://broad-dsde-mint-dev-teststorage/reference/HISAT2/genome_snp_tran.tar.gz",
"SmartSeq2SingleCell.genome_ref_fasta": "gs://broad-dsde-mint-dev-teststorage/reference/GRCh38_Gencode/GRCh38.primary_assembly.genome.fa",
"SmartSeq2SingleCell.hisat2_ref_trans_index": "gs://broad-dsde-mint-dev-teststorage/reference/HISAT2/gencode_v27_trans_rsem.tar.gz",
"SmartSeq2SingleCell.rsem_ref_index": "gs://broad-dsde-mint-dev-teststorage/reference/rsem_ref/gencode_v27_primary.tar",
"SmartSeq2SingleCell.gene_ref_flat": "gs://broad-dsde-mint-dev-teststorage/reference/GRCh38_gencode.v27.refFlat.txt",
"SmartSeq2SingleCell.rrna_intervals": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode.v27.rRNA.interval_list",
"SmartSeq2SingleCell.star_ref_index": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/GRCh38_GencodeV27_Primary.tar",
"SmartSeq2SingleCell.hisat2_ref_index": "gs://hca-dcp-mint-test-data/reference/HISAT2/genome_snp_tran.tar.gz",
"SmartSeq2SingleCell.genome_ref_fasta": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/GRCh38.primary_assembly.genome.fa",
"SmartSeq2SingleCell.hisat2_ref_trans_index": "gs://hca-dcp-mint-test-data/reference/HISAT2/gencode_v27_trans_rsem.tar.gz",
"SmartSeq2SingleCell.rsem_ref_index": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode_v27_primary.tar",
"SmartSeq2SingleCell.gene_ref_flat": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/GRCh38_gencode.v27.refFlat.txt",
"SmartSeq2SingleCell.hisat2_ref_name": "genome_snp_tran",
"SmartSeq2SingleCell.stranded":"NONE",
"SmartSeq2SingleCell.fastq1":"gs://broad-dsde-mint-dev-teststorage/patel_ap/SRR1294925_1.fastq.gz",
"SmartSeq2SingleCell.fastq2":"gs://broad-dsde-mint-dev-teststorage/patel_ap/SRR1294925_2.fastq.gz",
"SmartSeq2SingleCell.fastq1":"gs://hca-dcp-mint-test-data/smartseq2_single_sample/patel_ap/SRR1294925_1.fastq.gz",
"SmartSeq2SingleCell.fastq2":"gs://hca-dcp-mint-test-data/smartseq2_single_sample/patel_ap/SRR1294925_2.fastq.gz",
"SmartSeq2SingleCell.sample_name":"SRR1294925",
"SmartSeq2SingleCell.output_name":"SRR1294925"
}
6 changes: 3 additions & 3 deletions test/smartseq2_single_sample/pr/test_inputs.json
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{
"TestSmartSeq2SingleCellPR.gtf_file": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode.v27.primary_assembly.annotation.gtf",
"TestSmartSeq2SingleCellPR.hisat2_ref_trans_name": "gencode_v27_trans_rsem",
"TestSmartSeq2SingleCellPR.rrna_intervals": "gs://hca-dcp-mint-test-data/reference/gencode.v27.rRNA.interval_list",
"TestSmartSeq2SingleCellPR.rrna_intervals": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode.v27.rRNA.interval_list",
"TestSmartSeq2SingleCellPR.star_ref_index": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/GRCh38_GencodeV27_Primary.tar",
"TestSmartSeq2SingleCellPR.hisat2_ref_index": "gs://hca-dcp-mint-test-data/reference/HISAT2/genome_snp_tran.tar.gz",
"TestSmartSeq2SingleCellPR.genome_ref_fasta": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/GRCh38.primary_assembly.genome.fa",
"TestSmartSeq2SingleCellPR.hisat2_ref_trans_index": "gs://hca-dcp-mint-test-data/reference/HISAT2/gencode_v27_trans_rsem.tar.gz",
"TestSmartSeq2SingleCellPR.rsem_ref_index": "gs://hca-dcp-mint-test-data/reference/rsem_ref/gencode_v27_primary.tar",
"TestSmartSeq2SingleCellPR.gene_ref_flat": "gs://hca-dcp-mint-test-data/reference/GRCh38_gencode.v27.refFlat.txt",
"TestSmartSeq2SingleCellPR.rsem_ref_index": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode_v27_primary.tar",
"TestSmartSeq2SingleCellPR.gene_ref_flat": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/GRCh38_gencode.v27.refFlat.txt",
"TestSmartSeq2SingleCellPR.hisat2_ref_name": "genome_snp_tran",
"TestSmartSeq2SingleCellPR.stranded":"NONE",
"TestSmartSeq2SingleCellPR.fastq1":"gs://hca-dcp-mint-test-data/smartseq2_single_sample/patel_ap/SRR1294925_1.fastq.gz",
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