main_workflow_precursor_specific_fasta.nf

#!/usr/bin/env nextflow
nextflow.enable.dsl=2

// Required Parameters (Input-Files)
params.main_sp_embl_file = "" // The SP-EMBL file of the species to be searched (downloadable from UniProtKB)
params.main_raw_files_folder = ""  // The folder where the RAW-files are located.
params.main_comet_params = ""  // The comet parameter file for search. NOTE: Here the digestion needs to be explicitly set to "no_digestion", since the fasta is already digested (default: digestion is Trypsin)

// Optional Parameters
// See each nextflow script.

// Output Parameters which are fixed for the folder structure.
// NOTE: these can be changed and also individually turned off. See for the corresponding nextflow scripts
params.main_outdir = "$PWD/results"
params.ctm_outdir =  "${params.main_outdir}/mgfs"
params.cmf_outdir =  "${params.main_outdir}/fastas"
params.idc_outdir =  "${params.main_outdir}/identifications"
params.sir_outdir =  "${params.main_outdir}/statistics"

// Set Parameters, since we use a ms2-specific-FASTA (across a whole dataset) generated with ProtGraph
params.cmf_one_fasta = true
params.sir_identification_from_protgraph = true
params.sir_remove_variable_modifications = true
params.sir_count_same_protein_as_unique = true


// Import Workflows
PROJECT_DIR = workflow.projectDir
include {convert_to_mgf} from PROJECT_DIR + '/convert_to_mgf.nf'
include {create_precursor_specific_fasta} from PROJECT_DIR + '/create_precursor_specific_fasta.nf'
include {identification_via_comet} from PROJECT_DIR + '/identification_via_comet.nf'
include {summarize_ident_results} from PROJECT_DIR + '/summarize_ident_results.nf'


// Standalone MAIN Workflow
workflow {
	sp_embl_file = Channel.fromPath(params.main_sp_embl_file)
    raw_files = Channel.fromPath(params.main_raw_files_folder  + "/*.raw")
    comet_params = Channel.fromPath(params.main_comet_params)

    main_workflow_global_fasta(
        sp_embl_file,
        raw_files,
        comet_params
    )
}

// Importable MAIN Workflow
workflow main_workflow_global_fasta {
    take:
        sp_embl_file
        raw_files
        comet_parameters_file
    main:
        // Generate MGF-Files
        convert_to_mgf(raw_files)

        // Generate FASTA
        create_precursor_specific_fasta(convert_to_mgf.out, sp_embl_file) 

        // Search via Comet (+ Percolator if set)
        identification_via_comet(
            convert_to_mgf.out,
            create_precursor_specific_fasta.out,
            comet_parameters_file
        )

        // Group multiple FDRs
        grouped_fdrs = identification_via_comet.out.groupTuple()

        // For each FDR get the identification summaries
        final_grouped_results = grouped_fdrs.map { tuple("___" + it[0].toString() + "_fdr",  it [1]) }
        summarize_ident_results(final_grouped_results)
}