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.
28 lines
1.0 KiB
Plaintext
28 lines
1.0 KiB
Plaintext
nextflow.enable.dsl=2
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// STRING-only re-run workflow
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// Feeds existing ConPLex significant_interactions files into NETWORK_ENRICHMENT
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//
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// Required params:
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// interactions - directory containing *_significant_interactions.tsv files
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// interaction_ids - comma-separated InChIKey prefixes to select (e.g. "PWKSKIMOESPYIA_SCSAIBSYSA_N,ZETLRLRYANUSAI_SCSAIBSYSA_N")
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// if empty/not set, all files in the directory are used
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params.protein_network_threshold = 0.65
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include { NETWORK_ENRICHMENT } from './main_conplex.nf'
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workflow {
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if (params.interaction_ids) {
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// Build a channel from the explicit list of IDs
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ids = params.interaction_ids.tokenize(',')
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interactions_ch = Channel
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.fromList(ids)
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.map { id -> file("${params.interactions}/${id}_patient_0_significant_interactions.tsv") }
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} else {
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interactions_ch = Channel.fromPath("${params.interactions}/*_significant_interactions.tsv")
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}
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NETWORK_ENRICHMENT(interactions_ch)
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}
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