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403 lines (342 loc) · 16.2 KB
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{
"test_data_root": "~/Desktop/machine/omnibioai-test-data",
"bundles_root": "~/Desktop/machine/omnibioai-workflow-bundles",
"reference": {
"hg38_fasta": "reference/human/hg38/chr21_22.fa",
"hg38_fasta_full": "reference/human/hg38/hg38.fa.gz",
"hg38_fai": "reference/human/hg38/chr21_22.fa.fai",
"mm10_fasta": "reference/mouse/mm10/mm10.fa.gz",
"gtf_human": "reference/annotation/gencode.v44.annotation.gtf",
"gtf_mouse": "reference/annotation/gencode.vM25.annotation.gtf.gz",
"star_index": "reference/indices/star/hg38_chr21_22",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa",
"bismark_index": "reference/indices/bismark/hg38_chr21_22",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A",
"kraken2_db": "reference/databases/kraken2",
"silva_seqs": "reference/databases/silva/silva-138-99-seqs.qza",
"silva_tax": "reference/databases/silva/silva-138-99-tax.qza",
"dbsnp": "reference/databases/00-All.vcf.gz",
"clinvar": "reference/databases/clinvar.vcf.gz"
},
"domain_map": {
"rnaseq": {
"test_r1": "test_data/rnaseq/test_R1.fastq",
"test_r2": "test_data/rnaseq/test_R2.fastq",
"star_index": "reference/indices/star/hg38_chr21_22",
"gtf": "reference/annotation/gencode.v44.annotation.gtf",
"genome": "reference/human/hg38/chr21_22.fa",
"samplesheet": "auto-generate"
},
"rnaseq_v1": {
"test_r1": "test_data/rnaseq/test_R1.fastq",
"test_r2": "test_data/rnaseq/test_R2.fastq",
"star_index": "reference/indices/star/hg38_chr21_22",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"singlecell": {
"fastq_dir": "test_data/singlecell/pbmc_1k/pbmc_1k_v3_fastqs",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A",
"genome": "reference/human/hg38/chr21_22.fa",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"single_cell_multiome": {
"fastq_dir": "test_data/singlecell/pbmc_1k/pbmc_1k_v3_fastqs",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A"
},
"single_cell_multiomics": {
"fastq_dir": "test_data/singlecell/pbmc_1k/pbmc_1k_v3_fastqs",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A"
},
"single_cell_vdj": {
"fastq_dir": "test_data/singlecell/pbmc_1k/pbmc_1k_v3_fastqs",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A"
},
"scatac_seq": {
"test_r1": "test_data/atacseq/SRR5799393_1.fastq",
"test_r2": "test_data/atacseq/SRR5799393_2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa"
},
"atacseq": {
"test_r1": "test_data/atacseq/SRR5799393_1.fastq",
"test_r2": "test_data/atacseq/SRR5799393_2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"chipseq": {
"test_r1": "test_data/chipseq/SRR227563.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"epigenomics": {
"test_r1": "test_data/epigenomics/histone_H3K27ac_R1_001.fastq.gz",
"test_r2": "test_data/epigenomics/histone_H3K27ac_R2_001.fastq.gz",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa",
"bismark_index": "reference/indices/bismark/hg38_chr21_22",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"methylation": {
"test_r1": "test_data/methylation/SRR3368180_1.fastq",
"test_r2": "test_data/methylation/SRR3368180_2.fastq",
"bismark_index": "reference/indices/bismark/hg38_chr21_22",
"genome": "reference/human/hg38/chr21_22.fa"
},
"nanopore_methylation": {
"test_reads": "test_data/longread/nanopore_reads.fastq.gz",
"genome": "reference/human/hg38/chr21_22.fa"
},
"wgs": {
"test_r1": "test_data/wgs/NA12878_R1.fastq",
"test_r2": "test_data/wgs/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa",
"dbsnp": "reference/databases/00-All.vcf.gz",
"known_indels": "reference/databases/clinvar.vcf.gz"
},
"wes": {
"test_r1": "test_data/wes/NA12878_R1.fastq",
"test_r2": "test_data/wes/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa",
"dbsnp": "reference/databases/00-All.vcf.gz",
"known_indels": "reference/databases/clinvar.vcf.gz"
},
"exome_clinical": {
"test_r1": "test_data/wes/NA12878_R1.fastq",
"test_r2": "test_data/wes/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa",
"dbsnp": "reference/databases/00-All.vcf.gz"
},
"clinical": {
"test_r1": "test_data/wes/NA12878_R1.fastq",
"test_r2": "test_data/wes/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa",
"dbsnp": "reference/databases/00-All.vcf.gz",
"variants_tsv": "test_data/clinical/sample_variants.tsv",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"ctdna_analysis": {
"test_r1": "test_data/ctdna_analysis/NA12878_R1.fastq",
"test_r2": "test_data/ctdna_analysis/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa"
},
"sv": {
"test_r1": "test_data/sv/NA12878_R1.fastq",
"test_r2": "test_data/sv/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa"
},
"longread": {
"test_reads": "test_data/longread/nanopore_reads.fastq.gz",
"assembly_reads": "test_data/longread/assembly_reads.fasta.gz",
"genome": "reference/human/hg38/chr21_22.fa"
},
"long_read_rna": {
"test_reads": "test_data/longread/nanopore_reads.fastq.gz",
"genome": "reference/human/hg38/chr21_22.fa",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"ancient_dna": {
"test_r1": "test_data/wgs/NA12878_R1.fastq",
"test_r2": "test_data/wgs/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa"
},
"spatial": {
"fastq_r1": "test_data/spatial/visium_brain/V1_Brain_R1_001.fastq.gz",
"fastq_r2": "test_data/spatial/visium_brain/V1_Brain_R2_001.fastq.gz",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A",
"xenium_outs": "test_data/spatial/xenium/outs"
},
"spatial_hd": {
"xenium_outs": "test_data/spatial/xenium/outs",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A"
},
"spatial_multiomics": {
"fastq_r1": "test_data/spatial/visium_brain/V1_Brain_R1_001.fastq.gz",
"fastq_r2": "test_data/spatial/visium_brain/V1_Brain_R2_001.fastq.gz",
"xenium_outs": "test_data/spatial/xenium/outs"
},
"spatial_proteomics": {
"xenium_outs": "test_data/spatial/xenium/outs"
},
"microbiome": {
"test_r1": "test_data/microbiome/SRR2822457_1.fastq",
"test_r2": "test_data/microbiome/SRR2822457_2.fastq",
"reads_16s_r1": "test_data/microbiome/16S_R1.fastq.gz",
"reads_16s_r2": "test_data/microbiome/16S_R2.fastq.gz",
"kraken2_db": "reference/databases/kraken2",
"silva_seqs": "reference/databases/silva/silva-138-99-seqs.qza",
"silva_tax": "reference/databases/silva/silva-138-99-tax.qza"
},
"metagenomics": {
"test_r1": "test_data/metagenomics/community_R1.fastq.gz",
"test_r2": "test_data/metagenomics/community_R2.fastq.gz",
"kraken2_db": "reference/databases/kraken2"
},
"proteomics": {
"mzxml": "test_data/proteomics/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML"
},
"proteomics_ms": {
"mzxml": "test_data/proteomics/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML"
},
"crispr": {
"fastq": "test_data/crispr/demo.fastq.gz",
"library": "test_data/crispr/demo_library.txt",
"genome": "reference/human/hg38/chr21_22.fa"
},
"crispr_ml": {
"fastq": "test_data/crispr/demo.fastq.gz",
"library": "test_data/crispr/demo_library.txt"
},
"funcgen": {
"peaks_bed": "test_data/funcgen/peaks.bed",
"genome": "reference/human/hg38/chr21_22.fa",
"gtf": "reference/annotation/gencode.v44.annotation.gtf",
"test_r1": "test_data/wgs/NA12878_R1.fastq",
"test_r2": "test_data/wgs/NA12878_R2.fastq"
},
"multimodal": {
"cite_gex_r1": "test_data/multimodal/cite_seq_gex_R1_001.fastq.gz",
"cite_gex_r2": "test_data/multimodal/cite_seq_gex_R2_001.fastq.gz",
"cite_adt_r1": "test_data/multimodal/cite_seq_adt_R1_001.fastq.gz",
"cite_adt_r2": "test_data/multimodal/cite_seq_adt_R2_001.fastq.gz",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A",
"genome": "reference/human/hg38/chr21_22.fa",
"gtf": "reference/annotation/gencode.v44.annotation.gtf",
"mzxml": "test_data/proteomics/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML"
},
"multimodal_integration": {
"cite_gex_r1": "test_data/multimodal/cite_seq_gex_R1_001.fastq.gz",
"cite_gex_r2": "test_data/multimodal/cite_seq_gex_R2_001.fastq.gz",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A"
},
"multiomics": {
"rna_r1": "test_data/multiomics/rna_R1_R1_001.fastq.gz",
"rna_r2": "test_data/multiomics/rna_R1_R2_001.fastq.gz",
"atac_r1": "test_data/multiomics/atac_R1_R1_001.fastq.gz",
"atac_r2": "test_data/multiomics/atac_R1_R2_001.fastq.gz",
"genome": "reference/human/hg38/chr21_22.fa",
"star_index": "reference/indices/star/hg38_chr21_22",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"target_identification": {
"variants_vcf": "test_data/target_identification/variants.vcf",
"genome": "reference/human/hg38/chr21_22.fa"
},
"drug_response_prediction": {
"compounds_csv": "test_data/drug_discovery/compounds.csv"
},
"drug_synergy": {
"compounds_csv": "test_data/drug_discovery/compounds.csv"
},
"admet_prediction": {
"compounds_csv": "test_data/drug_discovery/compounds.csv"
},
"foundation_model": {
"sequences_fasta": "test_data/foundation_model/sequences.fasta",
"genome": "reference/human/hg38/chr21_22.fa"
},
"variant_ml": {
"variants_vcf": "test_data/target_identification/variants.vcf",
"genome": "reference/human/hg38/chr21_22.fa",
"dbsnp": "reference/databases/00-All.vcf.gz"
},
"polygenic_risk_score": {
"variants_vcf": "test_data/target_identification/variants.vcf",
"genome": "reference/human/hg38/chr21_22.fa"
},
"population_genetics": {
"test_r1": "test_data/wgs/NA12878_R1.fastq",
"test_r2": "test_data/wgs/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa"
},
"hla_typing": {
"test_r1": "test_data/wes/NA12878_R1.fastq",
"test_r2": "test_data/wes/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa"
},
"circrna": {
"test_r1": "test_data/rnaseq/test_R1.fastq",
"test_r2": "test_data/rnaseq/test_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"star_index": "reference/indices/star/hg38_chr21_22",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"lncrna_analysis": {
"test_r1": "test_data/rnaseq/test_R1.fastq",
"test_r2": "test_data/rnaseq/test_R2.fastq",
"star_index": "reference/indices/star/hg38_chr21_22",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"mirna_seq": {
"test_r1": "test_data/rnaseq/test_R1.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"rna_editing": {
"test_r1": "test_data/rnaseq/test_R1.fastq",
"test_r2": "test_data/rnaseq/test_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"star_index": "reference/indices/star/hg38_chr21_22"
},
"riboseq": {
"test_r1": "test_data/rnaseq/test_R1.fastq",
"star_index": "reference/indices/star/hg38_chr21_22",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"cite_seq": {
"cite_gex_r1": "test_data/multimodal/cite_seq_gex_R1_001.fastq.gz",
"cite_gex_r2": "test_data/multimodal/cite_seq_gex_R2_001.fastq.gz",
"cite_adt_r1": "test_data/multimodal/cite_seq_adt_R1_001.fastq.gz",
"cite_adt_r2": "test_data/multimodal/cite_seq_adt_R2_001.fastq.gz",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A"
},
"cellranger": {
"fastq_dir": "test_data/singlecell/pbmc_1k/pbmc_1k_v3_fastqs",
"cellranger_ref": "reference/indices/cellranger/refdata-gex-GRCh38-2020-A"
},
"hic_analysis": {
"test_r1": "test_data/wgs/NA12878_R1.fastq",
"test_r2": "test_data/wgs/NA12878_R2.fastq",
"genome": "reference/human/hg38/chr21_22.fa",
"bwa_index": "reference/indices/bwa/hg38_chr21_22/chr21_22.fa"
},
"pangenome": {
"genome": "reference/human/hg38/chr21_22.fa",
"assembly_reads": "test_data/longread/assembly_reads.fasta.gz"
},
"genome_assembly": {
"assembly_reads": "test_data/longread/assembly_reads.fasta.gz",
"test_reads": "test_data/longread/nanopore_reads.fastq.gz"
},
"immune_deconvolution": {
"test_r1": "test_data/rnaseq/test_R1.fastq",
"test_r2": "test_data/rnaseq/test_R2.fastq",
"star_index": "reference/indices/star/hg38_chr21_22",
"gtf": "reference/annotation/gencode.v44.annotation.gtf"
},
"pharmacogenomics": {
"variants_vcf": "test_data/target_identification/variants.vcf",
"genome": "reference/human/hg38/chr21_22.fa",
"dbsnp": "reference/databases/00-All.vcf.gz"
},
"clinical_trial_matching": {
"variants_tsv": "test_data/clinical/sample_variants.tsv"
},
"bio_kg": {
"sequences_fasta": "test_data/foundation_model/sequences.fasta",
"variants_vcf": "test_data/target_identification/variants.vcf"
},
"obsolete": {
"skip": true,
"reason": "Obsolete bundles — no tests, skip batch testing"
}
}
}