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Configure pipeline for WES execution on k8s cluster

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- Add main.nf as WES entry point with PVC-based paths
- Update nextflow.config with k8s/k8s_gpu profiles (eureka-pvc)
- Update params.json defaults to /omic/eureka/digital-patients/ paths
- Remove stageInMode 'copy' from corto and vcf2prot for k8s compat
- Add reassemble.nf for one-time chunk reassembly on PVC
This commit is contained in:
Olamide Isreal
2026-03-26 17:58:28 +01:00
parent 9e6a16c19b
commit 88627edc25
6 changed files with 371 additions and 325 deletions
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161
main.nf Normal file
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@@ -0,0 +1,161 @@
nextflow.enable.dsl=2
// ================= CONTAINER IMAGES ================================================================
params.container_borzoi = 'harbor.cluster.omic.ai/omic/digital-patients/borzoi:latest'
params.container_vcf2prot = 'harbor.cluster.omic.ai/omic/digital-patients/vcf2prot:latest'
params.container_rna2protexpression = 'harbor.cluster.omic.ai/omic/digital-patients/rna2protexpression:latest'
params.container_corto = 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
params.container_ecotyper = 'harbor.cluster.omic.ai/omic/digital-patients/ecotyper:latest'
params.container_synthea = 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf'
// Container options - empty for k8s (k8s handles GPU scheduling via pod specs)
params.containerOptions = ''
params.containerOptions_synthea = ''
params.containerOptions_borzoi = ''
params.containerOptions_rna2protexpression = ''
// =================================================================================================
// SYNTHEA
params.n_pat = 2
params.percent_male = 0.5
params.disease = 'schizophrenia'
params.project_name = 'test'
// CIBERSORT
params.cibersortx_username = "gabriel.richman.2009@anderson.ucla.edu"
params.cibersortx_token = "b5b39e563fb947df4cfd4843d40fdb99"
// ====================== FILEPATHS (PVC mount paths) ===============================================
params.imputed_store = '/omic/eureka/digital-patients/imputed'
params.pheno_store = '/omic/eureka/digital-patients/ukbb_phenotypes_filtered.csv'
params.regulon = '/omic/eureka/digital-patients/regulon.rda'
params.healthy_dir = '/omic/eureka/digital-patients/healthy'
params.synthea_support_dir = '/omic/eureka/digital-patients/supporting-data'
params.mane = '/omic/eureka/digital-patients/MANE.GRCh38.v1.3.update.tsv'
params.signature_matrix = '/omic/eureka/digital-patients/LM22_sourceGEP_ensg.txt'
params.outdir = '/omic/eureka/digital-patients/output'
params.ecotyper_outdir = "${params.outdir}/ecotyper"
// ====================== FILTERING PARAMETERS =====================================================
params.enable_filtering = true
params.top_n_variants = 500
params.top_n_genes = 1000
params.transcriptome_log2fc_threshold = 1.5
params.top_n_proteins = 500
params.top_n_immune_cells = 20
params.top_n_metabolites = 50
params.metabolome_pvalue_threshold = 0.05
// ====================== INCLUDES ================================================================
//SYNTHEA
include {get_disease_stats_no_patients} from './main_synthea.nf'
include {generate_m_variants_cudf} from './main_synthea.nf'
include {generate_f_variants_cudf} from './main_synthea.nf'
include {make_vcfs} from './main_synthea.nf'
include {generate_m_healthy_cudf} from './main_synthea.nf'
include {generate_f_healthy_cudf} from './main_synthea.nf'
//BORZOI
include {FILTER_VCF} from './main_borzoi.nf'
include {PREDICT_EXPRESSION} from './main_borzoi.nf'
include {CREATE_PROTEIN_CLUSTER} from './main_borzoi.nf'
//VCF2PROT
include {VCF2PROT} from './main_vcf2prot.nf'
//RNA2PROTEINEXPRESSION
include {RNA2PROTEXPRESSION} from './main_rna2proteinexpression'
//CORTO
include {CORTO} from './main_corto.nf'
//CIBERSORT
include {CONVERT_TO_TXT} from './main_cibersortx.nf'
include {CIBERSORTx_FRACTIONS} from './main_cibersortx.nf'
include {CIBERSORTx_HIRES} from './main_cibersortx.nf'
include {ADD_TISSUE_NAMES_TO_CIBERSORTX} from './main_cibersortx.nf'
//FILTERING PROCESSES
include {FILTER_VARIANTS} from './main_filter_outputs.nf'
include {FILTER_TRANSCRIPTOME} from './main_filter_outputs.nf'
include {FILTER_PROTEOME} from './main_filter_outputs.nf'
include {FILTER_IMMUNE_CELLS} from './main_filter_outputs.nf'
include {FILTER_METABOLOME} from './main_filter_outputs.nf'
include {FILTER_MUTATED_PROTEINS} from './main_filter_outputs.nf'
include {CREATE_SUMMARY_REPORT} from './main_filter_outputs.nf'
workflow {
pheno_store_ch = file(params.pheno_store)
imputed_store_ch = file(params.imputed_store)
synthea_support_ch = file(params.synthea_support_dir)
regulon_ch = file(params.regulon)
signature_matrix_ch = file(params.signature_matrix)
mane_ch = file(params.mane)
health_dir_ch = file(params.healthy_dir)
//SYNTHEA
switch (params.disease) {
case 'healthy':
generate_m_healthy_cudf(health_dir_ch)
generate_f_healthy_cudf(health_dir_ch)
m_healthy = generate_m_healthy_cudf.out
f_healthy = generate_f_healthy_cudf.out
txt_ch = f_healthy.mix(m_healthy).flatten()
break
default:
get_disease_stats_no_patients(pheno_store_ch, imputed_store_ch)
generate_m_variants_cudf(get_disease_stats_no_patients.out)
generate_f_variants_cudf(get_disease_stats_no_patients.out)
f_var = generate_f_variants_cudf.out
m_var = generate_m_variants_cudf.out
txt_ch = f_var.mix(m_var).flatten()
}
make_vcfs(txt_ch, synthea_support_ch)
//BORZOI
FILTER_VCF(mane_ch, make_vcfs.out)
PREDICT_EXPRESSION(FILTER_VCF.out, mane_ch)
//VCF2PROT
VCF2PROT(make_vcfs.out, FILTER_VCF.out)
//RNA2PROTEINEXPRESSION
PREDICT_EXPRESSION.out
.collect()
.flatten()
.set { rna_input }
RNA2PROTEXPRESSION(rna_input)
//CORTO
CORTO(PREDICT_EXPRESSION.out, regulon_ch)
//CIBERSORT
signature_file = Channel.fromPath(signature_matrix_ch, checkIfExists: true)
CONVERT_TO_TXT(PREDICT_EXPRESSION.out)
CIBERSORTx_FRACTIONS(CONVERT_TO_TXT.out, signature_file)
CIBERSORTx_HIRES(CONVERT_TO_TXT.out, CIBERSORTx_FRACTIONS.out, signature_file)
ADD_TISSUE_NAMES_TO_CIBERSORTX(CONVERT_TO_TXT.out, CIBERSORTx_HIRES.out)
// FILTERING STAGE
if (params.enable_filtering) {
FILTER_VARIANTS(make_vcfs.out)
FILTER_TRANSCRIPTOME(PREDICT_EXPRESSION.out)
FILTER_PROTEOME(RNA2PROTEXPRESSION.out)
FILTER_IMMUNE_CELLS(ADD_TISSUE_NAMES_TO_CIBERSORTX.out)
FILTER_METABOLOME(CORTO.out)
FILTER_MUTATED_PROTEINS(VCF2PROT.out, FILTER_VARIANTS.out.filtered_vcf)
CREATE_SUMMARY_REPORT(
FILTER_TRANSCRIPTOME.out,
FILTER_PROTEOME.out,
FILTER_IMMUNE_CELLS.out,
FILTER_METABOLOME.out,
FILTER_VARIANTS.out.filtered_vcf
)
}
}

1
main_corto.nf
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@@ -8,7 +8,6 @@ process CORTO {
publishDir "${params.outdir}/${params.project_name}", mode: 'copy'
// debug true
// maxForks 1
stageInMode 'copy'
input:
path TPM

1
main_vcf2prot.nf
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@@ -7,7 +7,6 @@ process VCF2PROT {
containerOptions "${params.containerOptions}"
// echo true
publishDir "${params.outdir}/vcf2prot", mode: 'copy'
stageInMode 'copy'
maxForks 1
input:

105
nextflow.config
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@@ -1,98 +1,47 @@
manifest {
name = 'digital patients'
name = 'digital-patients'
author = 'omic'
recurseSubmodules = true
homePage = 'https://gitlab.com/omic/next/registry/pipelines/digitalpatients'
homePage = 'https://trs-gitea.cluster.omic.ai/omic/digital-patients'
description = 'generative digital patients and multi-omics pipeline'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.3'
defaultBranch = 'master'
defaultBranch = 'main'
}
// docker {
// enabled = true
// temp = 'auto'
// }
// process {
// withLabel: 'gpu_process' {
// containerOptions = '--gpus all --rm'
// }
//
// withLabel: 'cpu_process' {
// containerOptions = '--rm'
// }
// }
def sharedPod = [
[env: 'NXF_DEBUG', value: '0'],
[label: 'omic-app', value: 'digitalpatients'],
[imagePullSecret: 'gitlab-registry-secret'],
[volumeClaim: 'avatar-new', mountPath: '/mnt/Avatar/'],
]
profiles {
standard {
docker {
docker.enabled = true
enabled = true
temp = 'auto'
}
}
k8s_gpu {
process {
executor = 'local'
withLabel: 'gpu_process' {
maxForks = 1 // Only one GPU task at a time on single GPU system
containerOptions = '--gpus all --rm'
}
withLabel: 'cpu_process' {
containerOptions = '--rm'
}
}
}
k8s {
process {
executor = 'k8s'
namespace = 'bioinformatics'
debug = true
pod = sharedPod
withLabel: 'gpu_process' {
pod = sharedPod + [
[nodeSelector: [gpu: 'yes', 'gpu-type': 'geforce-rtx-3090']]
]
pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
accelerator = [request: 1, type: 'nvidia.com/gpu']
}
docker {
enabled = true
}
k8s {
storageClaimName = 'eureka-pvc'
storageMountPath = '/omic/eureka'
}
}
workDir = "/mnt/dreamdock-data/digital-patient-data/work"
k8s {
serviceAccount = 'nextflow-sa'
namespace = 'bioinformatics'
storageClaimName = 'dreamdock-data'
storageMountPath = '/mnt/dreamdock-data'
pullPolicy = 'IfNotPresent'
cleanup = true // delete pods after Ctrl+C or finished?
// cleanup = false // delete pods after Ctrl+C or finished?
// RUN AS DIFFERENT USERS
// securityContext = [fsGroup: 1000]
// securityContext = [
// runAsUser: 1000,
// fsGroup: 1000,
// runAsNonRoot: true
// ]
process {
executor = 'k8s'
}
docker {
enabled = true
}
k8s {
storageClaimName = 'eureka-pvc'
storageMountPath = '/omic/eureka'
}
// Use container image
// process.container = 'harbor.cluster.omic.ai/omic/faiss-indexer:latest'
}
}

352
params.json
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@@ -1,6 +1,5 @@
{
"params": {
"// SYNTHEA PARAMETERS": {},
"n_pat": {
"type": "integer",
"description": "Number of patients to generate (must be >= 2)",
@@ -10,9 +9,7 @@
"var_name": "params.n_pat",
"examples": [2, 10, 100],
"pattern": "^[0-9]+$",
"validation": {
"min": 2
},
"validation": { "min": 2 },
"notes": "Minimum of 2 patients required (one male, one female)"
},
"percent_male": {
@@ -23,42 +20,9 @@
"pipeline_io": "parameter",
"var_name": "params.percent_male",
"examples": [0.0, 0.5, 1.0],
"pattern": "^0(\\.\\d+)?|1(\\.0)?$",
"validation": {
"min": 0.0,
"max": 1.0
},
"validation": { "min": 0.0, "max": 1.0 },
"notes": "Value must be between 0 and 1 inclusive"
},
"imputed_store": {
"type": "folder",
"description": "Path to imputed UKBB data",
"default": "/mnt/Avatar/imputed/ukbb/imputed",
"required": true,
"pipeline_io": "input",
"var_name": "params.imputed_store",
"examples": [
"/mnt/Avatar/imputed/ukbb/imputed",
"/rosalind/ukbb/imputed"
],
"pattern": ".*",
"validation": {},
"notes": "Directory containing imputed UKBB data"
},
"pheno_store": {
"type": "file",
"description": "Path to phenotype data file",
"default": "/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv",
"required": true,
"pipeline_io": "input",
"var_name": "params.pheno_store",
"examples": [
"/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv"
],
"pattern": ".*\\.csv$",
"validation": {},
"notes": "CSV file containing filtered UKBB phenotype data"
},
"disease": {
"type": "string",
"description": "Disease or condition to simulate",
@@ -66,83 +30,10 @@
"required": true,
"pipeline_io": "parameter",
"var_name": "params.disease",
"examples": [
"schizophrenia",
"healthy",
"leukaemia",
"Purpura and other haemorrhagic conditions"
],
"pattern": ".*",
"enum": [
"schizophrenia",
"healthy",
"leukaemia",
"Purpura and other haemorrhagic conditions"
],
"validation": {},
"examples": ["schizophrenia", "healthy", "leukaemia"],
"enum": ["schizophrenia", "healthy", "leukaemia", "Purpura and other haemorrhagic conditions"],
"notes": "Use 'healthy' for healthy individuals or specify a disease condition"
},
"healthy_dir": {
"type": "folder",
"description": "Path to healthy patient data directory",
"default": "/Workspace/next/registry/pipelines/digital_patient",
"required": true,
"pipeline_io": "input",
"var_name": "params.healthy_dir",
"examples": [
"/Workspace/next/registry/pipelines/digital_patient",
"/mnt/Avatar/digital_patient"
],
"pattern": ".*",
"validation": {},
"notes": "Directory containing data for healthy patient generation"
},
"outdir": {
"type": "folder",
"description": "Output directory for results",
"default": "/mnt/omic-next-apis/wes/digital_patients",
"required": true,
"pipeline_io": "output",
"var_name": "params.outdir",
"examples": [
"/mnt/OmicNAS/dd/digital_patient",
"/path/to/custom/output"
],
"pattern": ".*",
"validation": {},
"notes": "Directory where all pipeline results will be stored"
},
"// BORZOI PARAMETERS": {},
"container_borzoi": {
"type": "string",
"description": "Borzoi container image",
"default": "borzoi:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_borzoi",
"examples": [
"borzoi:latest",
"borzoi:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for Borzoi module"
},
"containerOptions": {
"type": "string",
"description": "Container runtime options",
"default": "--gpus all --rm -v /mnt:/mnt",
"required": false,
"pipeline_io": "parameter",
"var_name": "params.containerOptions",
"examples": [
"--gpus all --rm -v /mnt:/mnt",
"--rm -v /data:/data"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container runtime options for GPU usage and volume mounts"
},
"project_name": {
"type": "string",
"description": "Project identifier",
@@ -150,106 +41,92 @@
"required": true,
"pipeline_io": "parameter",
"var_name": "params.project_name",
"examples": [
"test",
"production",
"schizophrenia_study"
],
"pattern": ".*",
"validation": {},
"notes": "Identifier for the digital patient project"
"examples": ["test", "production", "schizophrenia_study"]
},
"imputed_store": {
"type": "folder",
"description": "Path to imputed UKBB data directory",
"default": "/omic/eureka/digital-patients/imputed",
"required": true,
"pipeline_io": "input",
"var_name": "params.imputed_store",
"examples": ["/omic/eureka/digital-patients/imputed"],
"notes": "Directory containing imputed UKBB GWAS .bgz files"
},
"pheno_store": {
"type": "file",
"description": "Path to phenotype data file",
"default": "/omic/eureka/digital-patients/ukbb_phenotypes_filtered.csv",
"required": true,
"pipeline_io": "input",
"var_name": "params.pheno_store",
"examples": ["/omic/eureka/digital-patients/ukbb_phenotypes_filtered.csv"],
"pattern": ".*\\.csv$",
"notes": "CSV file containing filtered UKBB phenotype data"
},
"healthy_dir": {
"type": "folder",
"description": "Path to healthy patient data directory (gnomad files)",
"default": "/omic/eureka/digital-patients/healthy",
"required": true,
"pipeline_io": "input",
"var_name": "params.healthy_dir",
"examples": ["/omic/eureka/digital-patients/healthy"],
"notes": "Directory containing gnomad.genomes.v4.1.sites.{male,female}.txt"
},
"synthea_support_dir": {
"type": "folder",
"description": "Path to Synthea supporting data (VCF templates, liftover, genome)",
"default": "/omic/eureka/digital-patients/supporting-data",
"required": true,
"pipeline_io": "input",
"var_name": "params.synthea_support_dir",
"examples": ["/omic/eureka/digital-patients/supporting-data"],
"notes": "Must contain vcf/vcf_template.vcf, ucsc-liftover/hg19ToHg38.over.chain.gz, genome/hg38.fa"
},
"mane": {
"type": "file",
"description": "Path to MANE reference file",
"default": "/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv",
"default": "/omic/eureka/digital-patients/MANE.GRCh38.v1.3.update.tsv",
"required": true,
"pipeline_io": "input",
"var_name": "params.mane",
"examples": [
"/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv"
],
"examples": ["/omic/eureka/digital-patients/MANE.GRCh38.v1.3.update.tsv"],
"pattern": ".*\\.tsv$",
"validation": {},
"notes": "MANE transcripts reference file in TSV format"
},
"// VCF2PROT PARAMETERS": {},
"container_vcf2prot": {
"type": "string",
"description": "VCF2PROT container image",
"default": "vcf2prot:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_vcf2prot",
"examples": [
"vcf2prot:latest",
"vcf2prot:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for VCF2PROT module"
},
"// RNA2PROTEINEXPRESSION PARAMETERS": {},
"container_rna2protexpression": {
"type": "string",
"description": "RNA2PROTEINEXPRESSION container image",
"default": "rna2protexpression:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_rna2protexpression",
"examples": [
"rna2protexpression:latest",
"rna2protexpression:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for RNA2PROTEINEXPRESSION module"
},
"containerOptions_rna2protexpression": {
"type": "string",
"description": "Container options for RNA2PROTEINEXPRESSION",
"default": "--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs",
"required": false,
"pipeline_io": "parameter",
"var_name": "params.containerOptions_rna2protexpression",
"examples": [
"--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container runtime options for RNA2PROTEINEXPRESSION with GPU and database volume mounts"
},
"// CORTO PARAMETERS": {},
"container_corto": {
"type": "string",
"description": "CORTO container image",
"default": "corto:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_corto",
"examples": [
"corto:latest",
"corto:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for CORTO module"
},
"regulon": {
"type": "file",
"description": "Path to regulon RDA file",
"default": "/Workspace/next/registry/pipelines/digital_patient/regulon.rda",
"default": "/omic/eureka/digital-patients/regulon.rda",
"required": true,
"pipeline_io": "input",
"var_name": "params.regulon",
"examples": [
"/Workspace/next/registry/pipelines/digital_patient/regulon.rda"
],
"examples": ["/omic/eureka/digital-patients/regulon.rda"],
"pattern": ".*\\.rda$",
"validation": {},
"notes": "Regulon data file in RDA format for CORTO module"
},
"// CIBERSORT PARAMETERS": {},
"signature_matrix": {
"type": "file",
"description": "Path to signature matrix file for CIBERSORTx",
"default": "/omic/eureka/digital-patients/LM22_sourceGEP_ensg.txt",
"required": true,
"pipeline_io": "input",
"var_name": "params.signature_matrix",
"examples": ["/omic/eureka/digital-patients/LM22_sourceGEP_ensg.txt"],
"pattern": ".*\\.txt$",
"notes": "Signature matrix file for CIBERSORTx analysis"
},
"outdir": {
"type": "folder",
"description": "Output directory for results",
"default": "/omic/eureka/digital-patients/output",
"required": true,
"pipeline_io": "output",
"var_name": "params.outdir",
"examples": ["/omic/eureka/digital-patients/output"],
"notes": "Directory where all pipeline results will be stored"
},
"cibersortx_username": {
"type": "string",
"description": "CIBERSORTx username for authentication",
@@ -257,11 +134,6 @@
"required": true,
"pipeline_io": "parameter",
"var_name": "params.cibersortx_username",
"examples": [
"gabriel.richman.2009@anderson.ucla.edu"
],
"pattern": "^[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\\.[a-zA-Z]{2,}$",
"validation": {},
"notes": "Username (email) for CIBERSORTx authentication"
},
"cibersortx_token": {
@@ -271,55 +143,55 @@
"required": true,
"pipeline_io": "parameter",
"var_name": "params.cibersortx_token",
"examples": [
"b5b39e563fb947df4cfd4843d40fdb99"
],
"pattern": "^[a-f0-9]{32}$",
"validation": {},
"notes": "Authentication token for CIBERSORTx API access"
},
"container_borzoi": {
"type": "string",
"description": "Borzoi container image",
"default": "harbor.cluster.omic.ai/omic/digital-patients/borzoi:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_borzoi"
},
"container_vcf2prot": {
"type": "string",
"description": "VCF2PROT container image",
"default": "harbor.cluster.omic.ai/omic/digital-patients/vcf2prot:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_vcf2prot"
},
"container_rna2protexpression": {
"type": "string",
"description": "RNA2PROTEINEXPRESSION container image",
"default": "harbor.cluster.omic.ai/omic/digital-patients/rna2protexpression:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_rna2protexpression"
},
"container_corto": {
"type": "string",
"description": "CORTO container image",
"default": "harbor.cluster.omic.ai/omic/digital-patients/corto:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_corto"
},
"container_ecotyper": {
"type": "string",
"description": "ECOTyper container image",
"default": "ecotyper:latest",
"description": "ECOTyper/CIBERSORTx container image",
"default": "harbor.cluster.omic.ai/omic/digital-patients/ecotyper:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_ecotyper",
"examples": [
"ecotyper:latest",
"ecotyper:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for ECOTyper module"
"var_name": "params.container_ecotyper"
},
"signature_matrix": {
"type": "file",
"description": "Path to signature matrix file",
"default": "/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt",
"container_synthea": {
"type": "string",
"description": "Synthea container image",
"default": "harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf",
"required": true,
"pipeline_io": "input",
"var_name": "params.signature_matrix",
"examples": [
"/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt"
],
"pattern": ".*\\.txt$",
"validation": {},
"notes": "Signature matrix file for CIBERSORTx analysis"
},
"ecotyper_outdir": {
"type": "folder",
"description": "Output directory for ECOTyper results",
"default": "/mnt/omic-next-apis/wes/digital-patients/ecotyper",
"required": true,
"pipeline_io": "output",
"var_name": "params.ecotyper_outdir",
"examples": [
"/mnt/OmicNAS/olamide/ecotyper/results/ecotyper"
],
"pattern": ".*",
"validation": {},
"notes": "Directory where ECOTyper results will be stored"
"pipeline_io": "parameter",
"var_name": "params.container_synthea"
}
}
}

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reassemble.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
// One-time script to reassemble chunked files on the PVC
// Run once, then delete. Not part of the main pipeline.
params.base_dir = '/omic/eureka/digital-patients'
params.outdir = '/omic/eureka/digital-patients'
process REASSEMBLE {
container 'alpine:latest'
executor 'local'
script:
"""
echo "=== Reassembling chunked files ==="
# hg38.fa (35 parts)
if [ -d "${params.base_dir}/supporting-data/genome/hg38.fa_parts" ]; then
echo "Reassembling hg38.fa..."
cat ${params.base_dir}/supporting-data/genome/hg38.fa_parts/part_* > ${params.base_dir}/supporting-data/genome/hg38.fa
echo " Done: \$(du -h ${params.base_dir}/supporting-data/genome/hg38.fa | cut -f1)"
fi
# gnomad male (12 parts)
if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts" ]; then
echo "Reassembling gnomad male..."
cat ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts/part_* > ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt
echo " Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt | cut -f1)"
fi
# gnomad female (12 parts)
if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts" ]; then
echo "Reassembling gnomad female..."
cat ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts/part_* > ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt
echo " Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt | cut -f1)"
fi
# F5_SCHIZO male (7 parts)
if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts" ]; then
echo "Reassembling F5_SCHIZO male..."
cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz
echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz | cut -f1)"
fi
# F5_SCHIZO female (7 parts)
if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts" ]; then
echo "Reassembling F5_SCHIZO female..."
cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz
echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz | cut -f1)"
fi
# F5_SCHIZO both_sexes (7 parts)
if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz_parts" ]; then
echo "Reassembling F5_SCHIZO both_sexes..."
cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz
echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz | cut -f1)"
fi
echo "=== All reassembly complete ==="
"""
}
workflow {
REASSEMBLE()
}