nextflow.enable.dsl=2

// STRING-only re-run workflow
// Feeds existing ConPLex significant_interactions files into NETWORK_ENRICHMENT
//
// Required params:
//   interactions  - directory containing *_significant_interactions.tsv files
//   interaction_ids - comma-separated InChIKey prefixes to select (e.g. "PWKSKIMOESPYIA_SCSAIBSYSA_N,ZETLRLRYANUSAI_SCSAIBSYSA_N")
//                     if empty/not set, all files in the directory are used

params.protein_network_threshold = 0.65

include { NETWORK_ENRICHMENT } from './main_conplex.nf'

workflow {
    if (params.interaction_ids) {
        // Build a channel from the explicit list of IDs
        ids = params.interaction_ids.tokenize(',')
        interactions_ch = Channel
            .fromList(ids)
            .map { id -> file("${params.interactions}/${id}_patient_0_significant_interactions.tsv") }
    } else {
        interactions_ch = Channel.fromPath("${params.interactions}/*_significant_interactions.tsv")
    }

    NETWORK_ENRICHMENT(interactions_ch)
}