main.nf

#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/proteinfold
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/nf-core/proteinfold
    Website: https://nf-co.re/proteinfold
    Slack  : https://nfcore.slack.com/channels/proteinfold
----------------------------------------------------------------------------------------
*/

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

if (params.mode.toLowerCase().split(",").contains("alphafold2")) {
    include { PREPARE_ALPHAFOLD2_DBS } from './subworkflows/local/prepare_alphafold2_dbs'
    include { ALPHAFOLD2             } from './workflows/alphafold2'
}
if (params.mode.toLowerCase().split(",").contains("colabfold")) {
    include { PREPARE_COLABFOLD_DBS } from './subworkflows/local/prepare_colabfold_dbs'
    include { COLABFOLD             } from './workflows/colabfold'
}
if (params.mode.toLowerCase().split(",").contains("esmfold")) {
    include { PREPARE_ESMFOLD_DBS } from './subworkflows/local/prepare_esmfold_dbs'
    include { ESMFOLD             } from './workflows/esmfold'
}
if (params.mode.toLowerCase().split(",").contains("rosettafold_all_atom")) {
    include { PREPARE_ROSETTAFOLD_ALL_ATOM_DBS  } from './subworkflows/local/prepare_rosettafold_all_atom_dbs'
    include { ROSETTAFOLD_ALL_ATOM              } from './workflows/rosettafold_all_atom'
}
if (params.mode.toLowerCase().split(",").contains("helixfold3")) {
    include { PREPARE_HELIXFOLD3_DBS    } from './subworkflows/local/prepare_helixfold3_dbs'
    include { HELIXFOLD3                } from './workflows/helixfold3'
}

include { PIPELINE_INITIALISATION          } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
include { PIPELINE_COMPLETION              } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
include { getColabfoldAlphafold2Params     } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
include { getColabfoldAlphafold2ParamsPath } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
include { POST_PROCESSING                  } from './subworkflows/local/post_processing'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    COLABFOLD PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

params.colabfold_alphafold2_params_link = getColabfoldAlphafold2Params()
params.colabfold_alphafold2_params_path = getColabfoldAlphafold2ParamsPath()

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// WORKFLOW: Run main analysis pipeline
//

ch_dummy_file = Channel.fromPath("$projectDir/assets/NO_FILE")

workflow NFCORE_PROTEINFOLD {

    take:
    samplesheet // channel: samplesheet read in from --input

    main:
    ch_samplesheet              = samplesheet
    ch_alphafold_top_ranked_pdb = Channel.empty()
    ch_colabfold_top_ranked_pdb = Channel.empty()
    ch_esmfold_top_ranked_pdb   = Channel.empty()
    ch_rosettafold_all_atom_top_ranked_pdb   = Channel.empty()
    ch_helixfold3_top_ranked_pdb   = Channel.empty()
    ch_multiqc                  = Channel.empty()
    ch_versions                 = Channel.empty()
    ch_report_input             = Channel.empty()
    ch_foldseek_db              = Channel.empty()
    requested_modes             = params.mode.toLowerCase().split(",")
    requested_modes_size        = requested_modes.size()

    //
    // WORKFLOW: Run alphafold2
    //
    if(requested_modes.contains("alphafold2")) {
        //
        // SUBWORKFLOW: Prepare Alphafold2 DBs
        //
        PREPARE_ALPHAFOLD2_DBS (
            params.alphafold2_db,
            params.full_dbs,
            params.bfd_path,
            params.small_bfd_path,
            params.alphafold2_params_path,
            params.mgnify_path,
            params.pdb70_path,
            params.pdb_mmcif_path,
            params.uniref30_alphafold2_path,
            params.uniref90_path,
            params.pdb_seqres_path,
            params.uniprot_path,
            params.bfd_link,
            params.small_bfd_link,
            params.alphafold2_params_link,
            params.mgnify_link,
            params.pdb70_link,
            params.pdb_mmcif_link,
            params.pdb_obsolete_link,
            params.uniref30_alphafold2_link,
            params.uniref90_link,
            params.pdb_seqres_link,
            params.uniprot_sprot_link,
            params.uniprot_trembl_link
        )
        ch_versions = ch_versions.mix(PREPARE_ALPHAFOLD2_DBS.out.versions)

        //
        // WORKFLOW: Run nf-core/alphafold2 workflow
        //
        ALPHAFOLD2 (
            ch_samplesheet,
            ch_versions,
            params.full_dbs,
            params.alphafold2_mode,
            params.alphafold2_model_preset,
            PREPARE_ALPHAFOLD2_DBS.out.params,
            PREPARE_ALPHAFOLD2_DBS.out.bfd.ifEmpty([]).first(),
            PREPARE_ALPHAFOLD2_DBS.out.small_bfd.ifEmpty([]).first(),
            PREPARE_ALPHAFOLD2_DBS.out.mgnify,
            PREPARE_ALPHAFOLD2_DBS.out.pdb70,
            PREPARE_ALPHAFOLD2_DBS.out.pdb_mmcif,
            PREPARE_ALPHAFOLD2_DBS.out.uniref30,
            PREPARE_ALPHAFOLD2_DBS.out.uniref90,
            PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres,
            PREPARE_ALPHAFOLD2_DBS.out.uniprot
        )
        ch_alphafold_top_ranked_pdb = ALPHAFOLD2.out.top_ranked_pdb
        ch_multiqc                  = ch_multiqc.mix(ALPHAFOLD2.out.multiqc_report.collect())
        ch_versions                 = ch_versions.mix(ALPHAFOLD2.out.versions)
        ch_report_input             = ch_report_input.mix(ALPHAFOLD2.out.pdb_msa)
    }

    //
    // WORKFLOW: Run colabfold
    //
    if(requested_modes.contains("colabfold")) {
        //
        // SUBWORKFLOW: Prepare Colabfold DBs
        //
        PREPARE_COLABFOLD_DBS (
            params.colabfold_db,
            params.colabfold_server,
            params.colabfold_alphafold2_params_path,
            params.colabfold_db_path,
            params.uniref30_colabfold_path,
            params.colabfold_alphafold2_params_link,
            params.colabfold_db_link,
            params.uniref30_colabfold_link,
            params.create_colabfold_index
        )
        ch_versions = ch_versions.mix(PREPARE_COLABFOLD_DBS.out.versions)

        //
        // WORKFLOW: Run nf-core/colabfold workflow
        //
        COLABFOLD (
            ch_samplesheet,
            ch_versions,
            params.colabfold_model_preset,
            PREPARE_COLABFOLD_DBS.out.params,
            PREPARE_COLABFOLD_DBS.out.colabfold_db,
            PREPARE_COLABFOLD_DBS.out.uniref30,
            params.num_recycles_colabfold
        )

        ch_colabfold_top_ranked_pdb = COLABFOLD.out.top_ranked_pdb
        ch_multiqc                  = ch_multiqc.mix(COLABFOLD.out.multiqc_report)
        ch_versions                 = ch_versions.mix(COLABFOLD.out.versions)
        ch_report_input             = ch_report_input.mix(COLABFOLD.out.pdb_msa)
    }

    //
    // WORKFLOW: Run esmfold
    //
    if(requested_modes.contains("esmfold")) {
        //
        // SUBWORKFLOW: Prepare esmfold DBs
        //
        PREPARE_ESMFOLD_DBS (
            params.esmfold_db,
            params.esmfold_params_path,
            params.esmfold_3B_v1,
            params.esm2_t36_3B_UR50D,
            params.esm2_t36_3B_UR50D_contact_regression
        )
        ch_versions = ch_versions.mix(PREPARE_ESMFOLD_DBS.out.versions)

        //
        // WORKFLOW: Run nf-core/esmfold workflow
        //
        ESMFOLD (
            ch_samplesheet,
            ch_versions,
            PREPARE_ESMFOLD_DBS.out.params,
            params.num_recycles_esmfold,
            ch_dummy_file
        )

        ch_esmfold_top_ranked_pdb = ESMFOLD.out.top_ranked_pdb
        ch_multiqc                = ch_multiqc.mix(ESMFOLD.out.multiqc_report.collect())
        ch_versions               = ch_versions.mix(ESMFOLD.out.versions)
        ch_report_input           = ch_report_input.mix(ESMFOLD.out.pdb_msa)
    }

    //
    // WORKFLOW: Run rosettafold_all_atom
    //
    if(requested_modes.contains("rosettafold_all_atom")) {
        //
        // SUBWORKFLOW: Prepare Rosettafold-all-atom DBs
        //
        PREPARE_ROSETTAFOLD_ALL_ATOM_DBS (
            params.rosettafold_all_atom_db,
            params.bfd_rosettafold_all_atom_path,
            params.uniref30_rosettafold_all_atom_path,
            params.pdb100_rosettafold_all_atom_path,
            params.rfaa_paper_weights_path,
            params.bfd_rosettafold_all_atom_link,
            params.uniref30_rosettafold_all_atom_link,
            params.pdb100_rosettafold_all_atom_link,
            params.rfaa_paper_weights_link
        )
        ch_versions = ch_versions.mix(PREPARE_ROSETTAFOLD_ALL_ATOM_DBS.out.versions)

        //
        // WORKFLOW: Run nf-core/rosettafold_all_atom workflow
        //
        ROSETTAFOLD_ALL_ATOM (
            ch_samplesheet,
            ch_versions,
            PREPARE_ROSETTAFOLD_ALL_ATOM_DBS.out.bfd,
            PREPARE_ROSETTAFOLD_ALL_ATOM_DBS.out.uniref30,
            PREPARE_ROSETTAFOLD_ALL_ATOM_DBS.out.pdb100,
            PREPARE_ROSETTAFOLD_ALL_ATOM_DBS.out.rfaa_paper_weights,
            ch_dummy_file
        )
        ch_rosettafold_all_atom_top_ranked_pdb  = ROSETTAFOLD_ALL_ATOM.out.top_ranked_pdb
        ch_multiqc                              = ch_multiqc.mix(ROSETTAFOLD_ALL_ATOM.out.multiqc_report.collect())
        ch_versions                             = ch_versions.mix(ROSETTAFOLD_ALL_ATOM.out.versions)
        ch_report_input                         = ch_report_input.mix(ROSETTAFOLD_ALL_ATOM.out.pdb_msa)
    }

    //
    // WORKFLOW: Run helixfold3
    //
    if(requested_modes.contains("helixfold3")) {
        //
        // SUBWORKFLOW: Prepare helixfold3 DBs
        //
        PREPARE_HELIXFOLD3_DBS (
            params.helixfold3_db,
            params.helixfold3_uniclust30_link,
            params.helixfold3_ccd_preprocessed_link,
            params.helixfold3_rfam_link,
            params.helixfold3_init_models_link,
            params.helixfold3_bfd_link,
            params.helixfold3_small_bfd_link,
            params.helixfold3_uniprot_sprot_link,
            params.helixfold3_uniprot_trembl_link,
            params.helixfold3_pdb_seqres_link,
            params.helixfold3_uniref90_link,
            params.helixfold3_mgnify_link,
            params.helixfold3_pdb_mmcif_link,
            params.helixfold3_pdb_obsolete_link,
            params.helixfold3_uniclust30_path,
            params.helixfold3_ccd_preprocessed_path,
            params.helixfold3_rfam_path,
            params.helixfold3_init_models_path,
            params.helixfold3_bfd_path,
            params.helixfold3_small_bfd_path,
            params.helixfold3_uniprot_path,
            params.helixfold3_pdb_seqres_path,
            params.helixfold3_uniref90_path,
            params.helixfold3_mgnify_path,
            params.helixfold3_pdb_mmcif_path,
            params.helixfold3_maxit_src_path
        )
        ch_versions = ch_versions.mix(PREPARE_HELIXFOLD3_DBS.out.versions)

        //
        // WORKFLOW: Run nf-core/helixfold3 workflow
        //
        HELIXFOLD3 (
            ch_samplesheet,
            ch_versions,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_uniclust30,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_ccd_preprocessed,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_rfam,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_bfd,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_small_bfd,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_uniprot,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_pdb_seqres,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_uniref90,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_mgnify,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_pdb_mmcif,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_init_models,
            PREPARE_HELIXFOLD3_DBS.out.helixfold3_maxit_src
        )
        ch_helixfold3_top_ranked_pdb    = HELIXFOLD3.out.top_ranked_pdb
        ch_multiqc                      = ch_multiqc.mix(HELIXFOLD3.out.multiqc_report.collect())
        ch_versions                     = ch_versions.mix(HELIXFOLD3.out.versions)
        ch_report_input                 = ch_report_input.mix(HELIXFOLD3.out.pdb_msa)
    }

    //
    // POST PROCESSING: generate visualisation reports
    //
    // TODO: we need to validate the rest of foldseek parameters if foldseek is set to run
    // TODO: maybe create a parameter that is run_foldseek or skip_foldsee instead as there are no more mode than can be use now

    // TODO move it to pdb.config? asign as in prepare dbs
    if (params.foldseek_search == "easysearch"){
        ch_foldseek_db = channel.value([
            [
                id: params.foldseek_db,
            ],
            file(params.foldseek_db_path, checkIfExists: true)
        ])
    }

    ch_multiqc_config        = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true).first()
    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ).first()  : Channel.empty()
    ch_multiqc_logo          = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo ).first()    : Channel.empty()
    ch_multiqc_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
    ch_report_template     = Channel.value(file("$projectDir/assets/report_template.html", checkIfExists: true))
    ch_comparison_template = Channel.value(file("$projectDir/assets/comparison_template.html", checkIfExists: true))

    POST_PROCESSING(
        params.skip_visualisation,
        params.mode,
        requested_modes_size,
        ch_report_input,
        ch_report_template,
        ch_comparison_template,
        params.foldseek_search,
        ch_foldseek_db,
        params.skip_multiqc,
        params.outdir,
        ch_versions,
        ch_multiqc,
        ch_multiqc_config,
        ch_multiqc_custom_config,
        ch_multiqc_logo,
        ch_multiqc_methods_description,
        ch_alphafold_top_ranked_pdb,
        ch_colabfold_top_ranked_pdb,
        ch_esmfold_top_ranked_pdb,
        ch_rosettafold_all_atom_top_ranked_pdb,
        ch_helixfold3_top_ranked_pdb
    )

    emit:
    multiqc_report = ch_multiqc
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

    main:
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input
    )

    //
    // WORKFLOW: Run main workflow
    //
    NFCORE_PROTEINFOLD (
        PIPELINE_INITIALISATION.out.samplesheet
    )

    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        NFCORE_PROTEINFOLD.out.multiqc_report
    )
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/