9e75f44f1a
Source-only snapshot of the cluster branch for WES execution. Large reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are omitted: they are baked into the container images at build time and mounted from the dreamdock-data PVC at runtime, and exceed the Gitea request size limit. Pipeline entry point is main.nf, which orchestrates the biotransformer, conplex and tissue modules as a single workflow. Ligand inputs are read from the eureka workspace; protein_zarr and chembl_db come from the dreamdock-data PVC.
58 lines
1.8 KiB
Plaintext
Executable File
58 lines
1.8 KiB
Plaintext
Executable File
nextflow.enable.dsl=2
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process TISSUE_DISTRIBUTION {
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memory { params.tissue_initial_memory.toInteger().GB + (task.attempt - 1) * params.tissue_growth_memory.toInteger().GB }
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container "${params.container_tissue}"
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// containerOptions "${params.containerOptions}"
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publishDir "${params.outdir}/${params.project_name}/4_tissue_distribution", mode: 'copy'
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// // Temporarily disabled debug prints
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// debug true
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errorStrategy { task.attempt <= params.tissue_max_retries.toInteger() ? 'retry' : params.tissue_fail_action }
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maxRetries params.tissue_max_retries.toInteger()
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input:
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path interaction
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output:
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path "*tissue_distribution.tsv", emit: tissue_dist
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script:
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"""
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# . activate tissue
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python /home/omic/drug_tissue_distribution.py --file_name ${interaction}
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"""
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}
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process BIO_METRICS {
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memory { params.bio_initial_memory.toInteger().GB + (task.attempt - 1) * params.bio_growth_memory.toInteger().GB }
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container "${params.container_tissue}"
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// containerOptions "${params.containerOptions}"
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publishDir "${params.outdir}/${params.project_name}/4_tissue_distribution", mode: 'copy'
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// debug true
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errorStrategy { task.attempt <= params.bio_max_retries.toInteger() ? 'retry' : params.bio_fail_action }
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maxRetries params.bio_max_retries.toInteger()
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input:
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tuple (
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val(id),
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path( target),
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path( metabolites),
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path( conplex_drug),
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path( conplex_all_interactions),
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)
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output:
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path "*_biological_properties.tsv", emit: bio_prop
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script:
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"""
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# . activate tissue
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python /home/omic/digital_patient_extract_metrics.py --metabolites ${metabolites} --conplex_all_interactions ${conplex_all_interactions} --conplex_drug ${conplex_drug} --target ${target}
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"""
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}
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