Olamide Isreal
4bbc9822af
- Update main.nf: hardcode Harbor container image, add workflow block, use PVC mount path defaults, remove stageInMode copy and legacy params - Update nextflow.config: add k8s profile with container, add process resource limits, update manifest to point to Gitea - Update params.json: use s3:// prefixed paths for WES, remove container_corto, containerOptions, and project_name params
43 lines
971 B
Plaintext
Executable File
43 lines
971 B
Plaintext
Executable File
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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// Parameters
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params.TPM = '/omic/eureka/corto/20002_1289_female_patient_0_TPM.csv'
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params.regulon = '/omic/eureka/corto/regulon.rda'
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params.outdir = '/omic/eureka/corto/output'
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process CORTO {
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container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
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publishDir params.outdir, mode: 'copy'
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debug true
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input:
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path TPM
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path regulon
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output:
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path "*_metabolome.csv", emit: csv_metabol
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script:
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"""
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#!/usr/bin/Rscript
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library(corto)
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library(data.table)
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TPM <- as.matrix(fread("$TPM"),rownames=1)
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load("$regulon")
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predicted<-mra(TPM, regulon=regulon)
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name = strsplit(strsplit("$TPM", split = "/")[[1]][length(strsplit("$TPM", split = "/")[[1]])], split = "_TPM.csv")[[1]][1]
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name = paste(name, "_metabolome.csv", sep="")
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write.csv(predicted, name)
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"""
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}
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workflow {
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CORTO(Channel.of(file(params.TPM)), Channel.of(file(params.regulon)))
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}
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