Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
103 lines
4.6 KiB
Plaintext
103 lines
4.6 KiB
Plaintext
nextflow.enable.dsl=2
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//SYNTHEA
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params.n_pat = 2//10 //number of patients to generate, must be => 2 (one male one female)
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params.percent_male = 0.5 // between 0-1, percant of mail patients
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//params.age = '18-80' //age range of the population, expressed as age-age
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//params.state = '"District of Columbia"' //'Hawaii' //'Texas' //'Georgia'
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//params.city = '' //'Washington' //'' //'Honolulu' //'Houston' //'Atlanta'
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params.imputed_store = '/mnt/Avatar/imputed/ukbb/imputed' //'/rosalind/ukbb/imputed'
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params.pheno_store = '/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv'
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params.disease = 'healthy' //'schizophrenia' //'healthy' //'leukaemia' //'leukaemia' //'Purpura and other haemorrhagic conditions' //['tongue cancer', 'dementia', 'arthritis'] //'tongue cancer' //'dementia'
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params.healthy_dir = '/Workspace/next/registry/pipelines/digital_patient' //'/mnt/Avatar/digital_patient' // data copy is here
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//params.n_var = 100
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params.outdir = '/mnt/OmicNAS/dd/digital_patient'
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//BORZOI
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params.container_borzoi = 'borzoi:latest'
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params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
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params.project_name = 'test'
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params.mane = '/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv'
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//VCF2PROT
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params.container_vcf2prot = "vcf2prot:latest"
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//RNA2PROTEINEXPRESSION
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params.container_rna2protexpression = 'rna2protexpression:latest'
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params.containerOptions_rna2protexpression = '--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs'
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//CORTO
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params.container_corto = 'corto:latest'
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params.regulon = '/Workspace/next/registry/pipelines/digital_patient/regulon.rda'
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//CIBERSORT
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params.cibersortx_username = "gabriel.richman.2009@anderson.ucla.edu"
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params.cibersortx_token = "b5b39e563fb947df4cfd4843d40fdb99"
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params.container_ecotyper = 'ecotyper:latest'
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params.signature_matrix = "/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt"
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params.ecotyper_outdir = "/mnt/OmicNAS/olamide/ecotyper/results/ecotyper"
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//SYNTHEA
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include {get_disease_stats_no_patients} from './main_synthea.nf'
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include {generate_m_variants_cudf} from './main_synthea.nf'
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include {generate_f_variants_cudf} from './main_synthea.nf'
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include {make_vcfs} from './main_synthea.nf'
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include {generate_m_healthy_cudf} from './main_synthea.nf'
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include {generate_f_healthy_cudf} from './main_synthea.nf'
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//BORZOI
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include {FILTER_VCF} from './main_borzoi.nf'
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include {PREDICT_EXPRESSION} from './main_borzoi.nf'
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include {CREATE_PROTEIN_CLUSTER} from './main_borzoi.nf'
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//VCF2PROT
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include {VCF2PROT} from './main_vcf2prot.nf'
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//RNA2PROTEINEXPRESSION
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include {RNA2PROTEXPRESSION} from './main_rna2proteinexpression'
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//CORTO
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include {CORTO} from './main_corto.nf'
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//CIBERSORT
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include {CONVERT_TO_TXT} from './main_cibersortx.nf'
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include {CIBERSORTx_FRACTIONS} from './main_cibersortx.nf'
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include {CIBERSORTx_HIRES} from './main_cibersortx.nf'
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include {ADD_TISSUE_NAMES_TO_CIBERSORTX} from './main_cibersortx.nf'
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workflow {
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//SYNTHEA
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switch (params.disease) {
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case 'healthy':
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//healthy
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generate_m_healthy_cudf(params.healthy_dir)
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generate_f_healthy_cudf(params.healthy_dir)
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m_healthy = generate_m_healthy_cudf.out
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f_healthy = generate_f_healthy_cudf.out
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txt_ch = f_healthy.mix(m_healthy).flatten()
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break
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default:
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//disease
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get_disease_stats_no_patients()
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generate_m_variants_cudf(get_disease_stats_no_patients.out)
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generate_f_variants_cudf(get_disease_stats_no_patients.out)
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f_var = generate_f_variants_cudf.out
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m_var = generate_m_variants_cudf.out
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txt_ch = f_var.mix(m_var).flatten()
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}
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make_vcfs(txt_ch)
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//BORZOI
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// Prepare the VCF file(s)
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//vcf_ch = Channel.fromPath(make_vcfs.out)
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// THIS IS USES TO CREATE PROTEIN CLUSTER ON A SAME BORZOI INPUT AND SPLI ONES TO BIG FOR BORZOI (LEN = 524288)
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// THIS STEP NEEDS TO BR RUN TO CREATE DATA FOR NEXT STEP ONLY IF NEW REFERENCE/RNAS ARE GOING TO BE USE
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//CREATE_PROTEIN_CLUSTER(params.mane)
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FILTER_VCF(params.mane, make_vcfs.out)
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PREDICT_EXPRESSION(FILTER_VCF.out, params.mane)
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//VCF2PROT
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VCF2PROT(make_vcfs.out, FILTER_VCF.out)
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//RNA2PROTEINEXPRESSION
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//collect is here onyl to stop RNA2PROTEXPRESSION run at the same time as BORZOI (not enough CUDA space)
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RNA2PROTEXPRESSION(PREDICT_EXPRESSION.out.collect())
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//CORTO
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CORTO(PREDICT_EXPRESSION.out, params.regulon)
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//CIBERSORT
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signature_file = Channel.fromPath(params.signature_matrix, checkIfExists: true)
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CONVERT_TO_TXT(PREDICT_EXPRESSION.out)
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CIBERSORTx_FRACTIONS(CONVERT_TO_TXT.out, signature_file)
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CIBERSORTx_HIRES(CONVERT_TO_TXT.out, CIBERSORTx_FRACTIONS.out, signature_file)
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ADD_TISSUE_NAMES_TO_CIBERSORTX(CONVERT_TO_TXT.out, CIBERSORTx_HIRES.out)
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}
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