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NAMES = {
'lane': 'Test1',
'lb': None,
'pu': 'Test1',
'sample': 'Test1',
'rg': 'Test1',
'pl': 'illumina'
}
DATA = {
'files': [
'/bcbio-nextgen/tests/test_automated_output/trimmed/1_1_Test1.trimmed.fq.gz',
'/bcbio-nextgen/tests/test_automated_output/trimmed/1_2_Test1.trimmed.fq.gz'
],
'dirs': {
'config': '/bcbio-nextgen/tests/test_automated_output',
'fastq': '/bcbio-nextgen/tests/data/test_fusion',
'work': '/bcbio-nextgen/tests/test_automated_output',
'flowcell': '/bcbio-nextgen/tests/data/test_fusion',
'galaxy': '/bcbio-nextgen/tests/data/automated'
},
'lane': '1',
'description': 'Test1',
'reference': {
'genome_context': [
'/bcbio-nextgen/tests/data/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz',
'/bcbio-nextgen/tests/data/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz'
],
'fasta': {
'base': '/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa'
},
'star': {
'indexes': [
'/bcbio-nextgen/tests/data/genomes/hg19/star/chrLength.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/sjdbList.out.tab',
'/bcbio-nextgen/tests/data/genomes/hg19/star/SA',
'/bcbio-nextgen/tests/data/genomes/hg19/star/Genome',
'/bcbio-nextgen/tests/data/genomes/hg19/star/SAindex',
'/bcbio-nextgen/tests/data/genomes/hg19/star/chrStart.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/chrName.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/chrNameLength.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/genomeParameters.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/Log.out'
]
},
'rtg': '/bcbio-nextgen/tests/data/genomes/hg19/rtg/hg19.sdf'
},
'sam_ref': '/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa',
'genome_resources': {
'rnaseq': {
'transcripts': '/bcbio-nextgen/tests/data/genomes/hg19/rnaseq/ref-transcripts.gtf',
'transcripts_mask': '/bcbio-nextgen/tests/data/genomes/hg19/rnaseq/ref-transcripts-mask.gtf',
'gene_bed': '/bcbio-nextgen/tests/data/genomes/hg19/rnaseq/ref-transcripts.bed'
},
'version': 7,
'variation': {
'train_omni': '/bcbio-nextgen/tests/data/genomes/hg19/variation/1000G_omni2.5.vcf.gz',
'dbnsfp': '/bcbio-nextgen/tests/data/genomes/hg19/variation/dbNSFP_v2.5.gz',
'cosmic': '/bcbio-nextgen/tests/data/genomes/hg19/variation/cosmic-v68-hg19.vcf.gz',
'ancestral': '/bcbio-nextgen/tests/data/genomes/hg19/variation/human_ancestor.fa',
'train_hapmap': '/bcbio-nextgen/tests/data/genomes/hg19/variation/hapmap_3.3.vcf.gz',
'train_1000g': '/bcbio-nextgen/tests/data/genomes/hg19/variation/1000G_phase1.snps.high_confidence.vcf.gz',
'dbsnp': '/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz',
'train_indels': '/bcbio-nextgen/tests/data/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz'
},
'srnaseq': {
'srna-trasncripts': '/bcbio-nextgen/tests/data/genomes/hg19/srnaseq/srna-transcripts.gtf',
'mirbase': '/bcbio-nextgen/tests/data/genomes/hg19/srnaseq/hairpin.fa'
},
'aliases': {
'snpeff': 'hg19',
'human': True,
'ensembl': 'homo_sapiens_vep_83_GRCh37'
}
},
'provenance': {
'data': '/bcbio-nextgen/tests/test_automated_output/provenance/data_versions.csv',
'entity': 'bcdd2c84-b800-11e6-a323-0242ac110002.prepare_sample.0.trim_sample.0.process_alignment.0',
'db': None,
'programs': '/bcbio-nextgen/tests/test_automated_output/provenance/programs.txt'
},
'rgnames': {
'lane': 'Test1',
'lb': None,
'pu': 'Test1',
'sample': 'Test1',
'rg': 'Test1',
'pl': 'illumina'
},
'upload': {
'dir': '/bcbio-nextgen/tests/test_automated_output/upload',
'run_id': ''
},
'analysis': 'RNA-seq',
'name': ['', 'Test1'],
'genome_build': 'hg19',
'config': {
'galaxy_config': '/bcbio-nextgen/tests/data/automated/universe_wsgi.ini',
'resources': {
'gatk': {
'jvm_opts': ['-Xms500m', '-Xmx3500m']
},
'default': {
'cores': 16,
'jvm_opts': ['-Xms750m', '-Xmx3500m'],
'memory': '3G'
},
'express': {'memory': '8g'},
'seqcluster': {'memory': '8g'},
'program_versions': '/bcbio-nextgen/tests/test_automated_output/provenance/programs.txt',
'dexseq': {'memory': '10g'},
'macs2': {'memory': '8g'},
'snpeff': {
'jvm_opts': ['-Xms750m', '-Xmx4g']
},
'qualimap': {'memory': '4g'}
},
'log_dir': '/var/log/bcbio',
'algorithm': {
'nomap_split_targets': 200,
'trim_reads': 'read_through',
'qc': ['fastqc', 'qualimap_rnaseq', 'samtools', 'gemini'],
'archive': [],
'recalibrate': False,
'mark_duplicates': True,
'nomap_split_size': 250,
'quality_format': 'illumina',
'aligner': 'star',
'validate_regions': None,
'realign': False,
'tools_off': [],
'fusion_mode': True,
'variant_regions': None,
'coverage_interval': None,
'adapters': ['truseq', 'polya'],
'validate': None, 'num_cores': 1, 'tools_on': []
},
'bcbio_system': '/bcbio-nextgen/tests/test_automated_output/bcbio_system-merged.yaml'
},
'resources': {},
'metadata': {
'batch': None,
'phenotype': ''
}
}
CONFIG = [[{'align_bam': '/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/Test1.bam',
'analysis': 'RNA-seq',
'config': {'algorithm': {'adapters': ['truseq', 'polya'],
'aligner': 'star',
'archive': [],
'coverage_interval': None,
'fusion_mode': True,
'mark_duplicates': True,
'nomap_split_size': 250,
'nomap_split_targets': 200,
'num_cores': 1,
'qc': ['fastqc',
'qualimap_rnaseq',
'samtools',
'gemini'],
'quality_format': 'illumina',
'realign': False,
'recalibrate': False,
'tools_off': [],
'tools_on': [],
'trim_reads': 'read_through',
'validate': None,
'validate_regions': None,
'variant_regions': None},
'bcbio_system': '/bcbio-nextgen/tests/test_automated_output/bcbio_system-merged.yaml',
'galaxy_config': '/bcbio-nextgen/tests/data/automated/universe_wsgi.ini',
'log_dir': '/var/log/bcbio',
'resources': {'default': {'cores': 16,
'jvm_opts': ['-Xms750m',
'-Xmx3500m'],
'memory': '3G'},
'dexseq': {'memory': '10g'},
'express': {'memory': '8g'},
'gatk': {'jvm_opts': ['-Xms500m',
'-Xmx3500m']},
'macs2': {'memory': '8g'},
'program_versions': '/bcbio-nextgen/tests/test_automated_output/provenance/programs.txt',
'qualimap': {'memory': '4g'},
'seqcluster': {'memory': '8g'},
'snpeff': {'jvm_opts': ['-Xms750m', '-Xmx4g']}}},
'description': 'Test1',
'dirs': {'config': '/bcbio-nextgen/tests/test_automated_output',
'fastq': '/bcbio-nextgen/tests/data/test_fusion',
'flowcell': '/bcbio-nextgen/tests/data/test_fusion',
'galaxy': '/bcbio-nextgen/tests/data/automated',
'work': '/bcbio-nextgen/tests/test_automated_output'},
'files': ['/bcbio-nextgen/tests/test_automated_output/trimmed/1_1_Test1.trimmed.fq.gz',
'/bcbio-nextgen/tests/test_automated_output/trimmed/1_2_Test1.trimmed.fq.gz'],
'genome_build': 'hg19',
'genome_resources': {'aliases': {'ensembl': 'homo_sapiens_vep_83_GRCh37',
'human': True,
'snpeff': 'hg19'},
'rnaseq': {'gene_bed': '/bcbio-nextgen/tests/data/genomes/hg19/rnaseq/ref-transcripts.bed',
'transcripts': '/bcbio-nextgen/tests/data/genomes/hg19/rnaseq/ref-transcripts.gtf',
'transcripts_mask': '/bcbio-nextgen/tests/data/genomes/hg19/rnaseq/ref-transcripts-mask.gtf'},
'srnaseq': {'mirbase': '/bcbio-nextgen/tests/data/genomes/hg19/srnaseq/hairpin.fa',
'srna-trasncripts': '/bcbio-nextgen/tests/data/genomes/hg19/srnaseq/srna-transcripts.gtf'},
'variation': {'ancestral': '/bcbio-nextgen/tests/data/genomes/hg19/variation/human_ancestor.fa',
'cosmic': '/bcbio-nextgen/tests/data/genomes/hg19/variation/cosmic-v68-hg19.vcf.gz',
'dbnsfp': '/bcbio-nextgen/tests/data/genomes/hg19/variation/dbNSFP_v2.5.gz',
'dbsnp': '/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz',
'train_1000g': '/bcbio-nextgen/tests/data/genomes/hg19/variation/1000G_phase1.snps.high_confidence.vcf.gz',
'train_hapmap': '/bcbio-nextgen/tests/data/genomes/hg19/variation/hapmap_3.3.vcf.gz',
'train_indels': '/bcbio-nextgen/tests/data/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz',
'train_omni': '/bcbio-nextgen/tests/data/genomes/hg19/variation/1000G_omni2.5.vcf.gz'},
'version': 7},
'hla': {'fastq': None},
'lane': '1',
'metadata': {'batch': None, 'phenotype': ''},
'name': ['', 'Test1'],
'provenance': {'data': '/bcbio-nextgen/tests/test_automated_output/provenance/data_versions.csv',
'db': None,
'entity': '21efc524-bc79-11e6-a323-0242ac110002.prepare_sample.0.trim_sample.0.process_alignment.0',
'programs': '/bcbio-nextgen/tests/test_automated_output/provenance/programs.txt'},
'reference': {'fasta': {'base': '/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa'},
'genome_context': ['/bcbio-nextgen/tests/data/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz',
'/bcbio-nextgen/tests/data/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz'],
'rtg': '/bcbio-nextgen/tests/data/genomes/hg19/rtg/hg19.sdf',
'star': {'indexes': ['/bcbio-nextgen/tests/data/genomes/hg19/star/chrLength.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/sjdbList.out.tab',
'/bcbio-nextgen/tests/data/genomes/hg19/star/SA',
'/bcbio-nextgen/tests/data/genomes/hg19/star/Genome',
'/bcbio-nextgen/tests/data/genomes/hg19/star/SAindex',
'/bcbio-nextgen/tests/data/genomes/hg19/star/chrStart.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/chrName.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/chrNameLength.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/genomeParameters.txt',
'/bcbio-nextgen/tests/data/genomes/hg19/star/Log.out']}},
'resources': {},
'rgnames': {'lane': 'Test1',
'lb': None,
'pl': 'illumina',
'pu': 'Test1',
'rg': 'Test1',
'sample': 'Test1'},
'sam_ref': '/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa',
'transcriptome_bam': None,
'upload': {'dir': '/bcbio-nextgen/tests/test_automated_output/upload',
'run_id': ''},
'work_bam': '/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/Test1.bam'}]]
|
