eager/subworkflows/local/deduplicate.nf at 5b1c505608ffcb1318bfb92eb21104da13e24340 · nf-core/eager · GitHub

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//
//  Carry out per-chromosome deduplication
//

include { addNewMetaFromAttributes                        } from '../../subworkflows/local/utils_nfcore_eager_pipeline/main'

include { BUILD_INTERVALS                                 } from '../../modules/local/build_intervals'
include { BAM_SPLIT_BY_REGION                             } from '../../subworkflows/nf-core/bam_split_by_region/main'
include { PICARD_MARKDUPLICATES                           } from '../../modules/nf-core/picard/markduplicates/main'
include { DEDUP                                           } from '../../modules/nf-core/dedup/main'
include { SAMTOOLS_MERGE    as SAMTOOLS_MERGE_DEDUPPED    } from '../../modules/nf-core/samtools/merge/main'
include { SAMTOOLS_SORT     as SAMTOOLS_SORT_DEDUPPED     } from '../../modules/nf-core/samtools/sort/main'
include { SAMTOOLS_INDEX    as SAMTOOLS_INDEX_DEDUPPED    } from '../../modules/nf-core/samtools/index/main'
include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT_DEDUPPED } from '../../modules/nf-core/samtools/flagstat/main'

workflow DEDUPLICATE {
    take:
    ch_bam_bai  // [ [ meta ], bam , bai ]
    fasta       // [ [ meta ], fasta ]
    fasta_fai   // [ [ meta ], fasta_fai ]

    main:
    ch_versions = Channel.empty()
    ch_multiqc_files  = Channel.empty()

    ch_refs = fasta.join(fasta_fai)
    .map {
        // Prepend a new meta that contains the meta.id value as the new_meta.reference attribute
        addNewMetaFromAttributes( it, "id" , "reference" , false )
    }

    // Create genomic regions file for splitting the bam before deduplication
    BUILD_INTERVALS( fasta_fai )
    ch_versions      = ch_versions.mix( BUILD_INTERVALS.out.versions.first() )

    // Prep regions for combining
    ch_intervals_for_join = BUILD_INTERVALS.out.bed
    .map {
        // Replace meta with new meta that contains the meta.id value in the meta.reference attribute only
        addNewMetaFromAttributes( it, "id" , "reference" , true )
    }

    // Ensure input bam matches the regions file
    ch_bam_for_split = ch_bam_bai
        .map {
            // Prepend a new meta that contains the meta.reference value as the new_meta.reference attribute
            addNewMetaFromAttributes( it, "reference" , "reference" , false )
        }
        .combine(
            by: 0,
            ch_intervals_for_join
        )
        .map {
            ignore_me, meta, bam, bai, regions ->
            [ meta, bam, bai, regions ]
        }

    //Split input bam by region
    BAM_SPLIT_BY_REGION( ch_bam_for_split )
    ch_versions   = ch_versions.mix( BAM_SPLIT_BY_REGION.out.versions )

    if ( params.deduplication_tool == 'markduplicates' ) {

        ch_markduplicates_input = BAM_SPLIT_BY_REGION.out.bam_bai
            .map {
                // Prepend a new meta that contains the meta.reference value as the new_meta.reference attribute
                addNewMetaFromAttributes( it, "reference" , "reference" , false )
            }
            .combine(
                by:0,
                ch_refs
            )
            .multiMap{
                ignore_me, meta, bam, bai, meta2, fasta_, fasta_fai_ ->
                bam: [ meta, bam ]
                fasta: [ meta2, fasta_ ]
                fasta_fai: [ meta2, fasta_fai_ ]
            }

            // Dedup each bam
            PICARD_MARKDUPLICATES(
                ch_markduplicates_input.bam,
                ch_markduplicates_input.fasta,
                ch_markduplicates_input.fasta_fai
            )
            ch_versions             = ch_versions.mix( PICARD_MARKDUPLICATES.out.versions.first() )

            ch_dedupped_region_bam  = PICARD_MARKDUPLICATES.out.bam

    } else if ( params.deduplication_tool == "dedup" ) {
        ch_dedup_input = BAM_SPLIT_BY_REGION.out.bam_bai
            .map {
                meta, bam, bai ->
                [ meta, bam ]
            }

        DEDUP( ch_dedup_input )
        ch_versions            = ch_versions.mix( DEDUP.out.versions.first() )

        ch_dedupped_region_bam = DEDUP.out.bam
    }

    ch_input_for_samtools_merge = ch_dedupped_region_bam
        .map {
            meta, bam ->
            def meta2 = meta.clone().findAll{ it.key != 'genomic_region' }
            [ meta2, bam ]
        }
        .groupTuple()
        .map {
            // Prepend a new meta that contains the meta.reference value as the new_meta.reference attribute
            addNewMetaFromAttributes( it, "reference" , "reference" , false )
        }
        .combine(
            by:0,
            ch_refs
        )
        .multiMap{
            // bam here is a list of bams
            ignore_me, meta, bam, meta2, fasta_, fasta_fai_ ->
            bam:        [ meta, bam ]
            fasta:      [ meta2, fasta_ ]
            fasta_fai:  [ meta2, fasta_fai_ ]
        }

    // Merge the bams for each region into one bam
    SAMTOOLS_MERGE_DEDUPPED(
        ch_input_for_samtools_merge.bam,
        ch_input_for_samtools_merge.fasta,
        ch_input_for_samtools_merge.fasta_fai
    )
    ch_versions   = ch_versions.mix( SAMTOOLS_MERGE_DEDUPPED.out.versions )


    // Sort the merged bam and index
    SAMTOOLS_SORT_DEDUPPED ( SAMTOOLS_MERGE_DEDUPPED.out.bam )
    ch_versions   = ch_versions.mix( SAMTOOLS_SORT_DEDUPPED.out.versions )
    ch_dedup_bam  = SAMTOOLS_SORT_DEDUPPED.out.bam

    SAMTOOLS_INDEX_DEDUPPED ( ch_dedup_bam )
    ch_versions   = ch_versions.mix( SAMTOOLS_INDEX_DEDUPPED.out.versions )
    ch_dedup_bai  =  params.fasta_largeref ? SAMTOOLS_INDEX_DEDUPPED.out.csi : SAMTOOLS_INDEX_DEDUPPED.out.bai

    // Finally run flagstat on the dedupped bam
    ch_input_for_samtools_flagstat = ch_dedup_bam.join( ch_dedup_bai )

    SAMTOOLS_FLAGSTAT_DEDUPPED(
        ch_input_for_samtools_flagstat
    )
    ch_versions       = ch_versions.mix( SAMTOOLS_FLAGSTAT_DEDUPPED.out.versions )
    ch_multiqc_files  = ch_multiqc_files.mix( SAMTOOLS_FLAGSTAT_DEDUPPED.out.flagstat )
    ch_dedup_flagstat = SAMTOOLS_FLAGSTAT_DEDUPPED.out.flagstat

    emit:
    bam         = ch_dedup_bam
    bai         = ch_dedup_bai
    flagstat    = ch_dedup_flagstat
    versions    = ch_versions
    mqc         = ch_multiqc_files
}