reference_indexing.nf

//
// Prepare reference indexing for downstream
//

include { REFERENCE_INDEXING_SINGLE } from '../../subworkflows/local/reference_indexing_single.nf'
include { REFERENCE_INDEXING_MULTI  } from '../../subworkflows/local/reference_indexing_multi.nf'
include { GUNZIP as GUNZIP_PMDBED   } from '../../modules/nf-core/gunzip/main.nf'
include { GUNZIP as GUNZIP_PMDFASTA } from '../../modules/nf-core/gunzip/main.nf'
include { GUNZIP as GUNZIP_SNPBED   } from '../../modules/nf-core/gunzip/main.nf'

workflow REFERENCE_INDEXING {
    take:
    fasta // file: /path/to/samplesheet.csv
    fasta_fai
    fasta_dict
    fasta_mapperindexdir

    main:
    ch_versions = Channel.empty()

    // Warn user if they've given a reference sheet that already includes fai/dict/mapper index etc.
    if ( ( fasta.extension == 'csv' || fasta.extension == 'tsv' ) && (fasta_fai || fasta_dict || fasta_mapperindexdir)) log.warn("A TSV or CSV has been supplied to `--fasta` as well as e.g. `--fasta_fai`. --fasta CSV/TSV takes priority and --fasta_* parameters will be ignored.")
    if ( ( fasta.extension == 'csv' || fasta.extension == 'tsv' ) && (params.mitochondrion_header || params.contamination_estimation_angsd_hapmap || params.damage_manipulation_pmdtools_reference_mask || params.snpcapture_bed || params.mapstats_bedtools_featurefile )) log.warn("A TSV or CSV has been supplied to `--fasta` as well as individual reference-specific input files, e.g. `--contamination_estimation_angsd_hapmap`. Input files specified in the --fasta CSV/TSV take priority and other input parameters will be ignored.")

    if ( fasta.extension == 'csv' || fasta.extension == 'tsv' ) {
        // If input (multi-)reference sheet supplied
        REFERENCE_INDEXING_MULTI ( fasta )
        ch_reference_for_mapping = REFERENCE_INDEXING_MULTI.out.reference
        ch_mitochondrion_header  = REFERENCE_INDEXING_MULTI.out.mitochondrion_header
        ch_hapmap                = REFERENCE_INDEXING_MULTI.out.hapmap
        ch_pmd_masked_fasta      = REFERENCE_INDEXING_MULTI.out.pmd_masked_fasta
        ch_pmd_bed_for_masking   = REFERENCE_INDEXING_MULTI.out.pmd_bed_for_masking
        ch_snp_capture_bed       = REFERENCE_INDEXING_MULTI.out.snp_capture_bed
        ch_pileupcaller_bed_snp  = REFERENCE_INDEXING_MULTI.out.pileupcaller_bed_snp
        ch_sexdeterrmine_bed     = REFERENCE_INDEXING_MULTI.out.sexdeterrmine_bed
        ch_bedtools_feature      = REFERENCE_INDEXING_MULTI.out.bedtools_feature
        ch_dbsnp                 = REFERENCE_INDEXING_MULTI.out.dbsnp
        ch_versions = ch_versions.mix( REFERENCE_INDEXING_MULTI.out.versions )
    } else {
        // If input FASTA and/or indicies supplied
        REFERENCE_INDEXING_SINGLE ( fasta, fasta_fai, fasta_dict, fasta_mapperindexdir )
        ch_mitochondrion_header  = REFERENCE_INDEXING_SINGLE.out.mitochondrion_header
        ch_hapmap                = REFERENCE_INDEXING_SINGLE.out.hapmap
        ch_pmd_masked_fasta      = REFERENCE_INDEXING_SINGLE.out.pmd_masked_fasta
        ch_pmd_bed_for_masking   = REFERENCE_INDEXING_SINGLE.out.pmd_bed_for_masking
        ch_snp_capture_bed       = REFERENCE_INDEXING_SINGLE.out.snp_capture_bed
        ch_pileupcaller_bed_snp  = REFERENCE_INDEXING_SINGLE.out.pileupcaller_bed_snp
        ch_sexdeterrmine_bed     = REFERENCE_INDEXING_SINGLE.out.sexdeterrmine_bed
        ch_bedtools_feature      = REFERENCE_INDEXING_SINGLE.out.bedtools_feature
        ch_reference_for_mapping = REFERENCE_INDEXING_SINGLE.out.reference
        ch_dbsnp                 = REFERENCE_INDEXING_SINGLE.out.dbsnp
        ch_versions = ch_versions.mix( REFERENCE_INDEXING_SINGLE.out.versions )
    }

    // Filter out input options that are not provided and unzip if necessary
    ch_mitochondrion_header = ch_mitochondrion_header
                    .filter{ it[1] != "" }

    ch_hapmap = ch_hapmap
                    .filter{ it[1] != "" }

    ch_pmd_masked_fasta = ch_pmd_masked_fasta
                    .branch {
                        meta, pmd_masked_fasta ->
                        input: pmd_masked_fasta != ""
                        skip: true
                    }
    ch_pmd_masked_fasta_gunzip = ch_pmd_masked_fasta.input
                    .branch {
                        meta, pmd_masked_fasta ->
                        forgunzip: pmd_masked_fasta.extension == "gz"
                        skip: true
                    }
    GUNZIP_PMDFASTA( ch_pmd_masked_fasta_gunzip.forgunzip )
    ch_pmd_masked_fasta = ch_pmd_masked_fasta_gunzip.skip.mix( GUNZIP_PMDFASTA.out.gunzip ).mix( ch_pmd_masked_fasta.skip )
    ch_version = ch_versions.mix( GUNZIP_PMDFASTA.out.versions.first() )

    ch_pmd_bed_for_masking = ch_pmd_bed_for_masking
                    .branch {
                        meta, pmd_bed_for_masking ->
                        input: pmd_bed_for_masking != ""
                        skip: true
                    }
    ch_pmd_bed_for_masking_gunzip = ch_pmd_bed_for_masking.input
                    .branch {
                        meta, pmd_bed_for_masking ->
                        forgunzip: pmd_bed_for_masking.extension == "gz"
                        skip: true
                    }
    GUNZIP_PMDBED( ch_pmd_bed_for_masking_gunzip.forgunzip )
    ch_pmd_bed_for_masking = ch_pmd_bed_for_masking_gunzip.skip.mix( GUNZIP_PMDBED.out.gunzip ).mix( ch_pmd_bed_for_masking.skip )
    ch_version = ch_versions.mix( GUNZIP_PMDBED.out.versions.first() )

    ch_pmd_masking = ch_pmd_masked_fasta
                    .combine( by: 0, ch_pmd_bed_for_masking )

    ch_capture_bed = ch_snp_capture_bed //bed file input is optional, so no filtering
                    .branch {
                        meta, capture_bed ->
                        input: capture_bed != ""
                        skip: true
                    }
    ch_capture_bed_gunzip = ch_capture_bed.input //unzip
                    .branch {
                        meta, capture_bed ->
                        forgunzip: capture_bed.extension == "gz"
                        skip: true
                    }
    GUNZIP_SNPBED( ch_capture_bed_gunzip.forgunzip )
    ch_capture_bed = GUNZIP_SNPBED.out.gunzip.mix( ch_capture_bed_gunzip.skip ).mix( ch_capture_bed.skip )
    ch_version = ch_versions.mix( GUNZIP_SNPBED.out.versions.first() )

    ch_pileupcaller_bed_snp = ch_pileupcaller_bed_snp
                    .filter { it[1] != "" || it[2] != "" } // They go together or not at all.
                    // Check if the channel is empty, and throw an error. Will only trigger for tsv fasta input. Single reference gets validated immediately.
                    .ifEmpty { if(params.run_genotyping && params.genotyping_tool == 'pileupcaller') { error "[nf-core/eager] ERROR: Genotyping with pileupcaller requires that both '--genotyping_pileupcaller_bedfile' AND '--genotyping_pileupcaller_snpfile' are provided for at least one reference genome." } }
                    .filter{ it != null } // Remove null channel which arises if empty cause error returns null.

    ch_sexdeterrmine_bed = ch_sexdeterrmine_bed
                    .filter { it[1] != "" }

    ch_bedtools_feature = ch_bedtools_feature
                    .filter { it[1] != "" }

    ch_dbsnp = ch_dbsnp
        .filter { it[1] != "" }

    emit:
    reference            = ch_reference_for_mapping // [ meta, fasta, fai, dict, mapindex, circular_target ]
    mitochondrion_header = ch_mitochondrion_header  // [ meta, mitochondrion_header ]
    hapmap               = ch_hapmap                // [ meta, hapmap ]
    pmd_masking          = ch_pmd_masking           // [ meta, pmd_masked_fasta, pmd_bed_for_masking ]
    pmd_bed_for_masking  = ch_pmd_bed_for_masking   // [ meta, pmd_bed_for_masking ]
    snp_capture_bed      = ch_capture_bed           // [ meta, capture_bed ]
    pileupcaller_bed_snp = ch_pileupcaller_bed_snp  // [ meta, pileupcaller_bed, pileupcaller_snp ]
    sexdeterrmine_bed    = ch_sexdeterrmine_bed     // [ meta, sexdet_bed ]
    bedtools_feature     = ch_bedtools_feature      // [ meta, bedtools_feature ]
    dbsnp                = ch_dbsnp                 // [ meta, dbsnp ]
    versions             = ch_versions

}