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

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//
// Run circularmapper
//

include { FASTQ_ALIGN_BWAALN as FASTQ_ALIGN_BWAALN_ELONGATED } from '../../subworkflows/nf-core/fastq_align_bwaaln/main'
include { CIRCULARMAPPER_REALIGNSAMFILE                      } from '../../modules/nf-core/circularmapper/realignsamfile/main'
include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_REALIGNED         } from '../../modules/nf-core/samtools/index/main'
include { addNewMetaFromAttributes                           } from '../../subworkflows/local/utils_nfcore_eager_pipeline/main'

workflow CIRCULARMAPPER {
    take:
    ch_reference            // channel (mandatory): [ val(meta), path(index), path(reference) ]
    ch_elongated_reference  // channel (mandatory): [ val(meta), path(elongated_index) ]
    ch_elongated_chr_list   // channel (mandatory): [ val(meta), path(elongated_chr_list) ]
    ch_fastq_reads          // channel (mandatory): [ val(meta), path(reads) ]. subworkImportant: meta REQUIRES single_end` entry!
    val_elongation_factor   //     int (mandatory): Elongation factor used for chromosome circularisation

    main:
    ch_versions       = Channel.empty()
    ch_multiqc_files  = Channel.empty()
    ch_realigned_bams = Channel.empty()
    ch_realigned_bais = Channel.empty()
    ch_realigned_csis = Channel.empty()

    // Although mapping with BWA will need the elongated reference index, RealignSAMFile apparently does NOT need the elongated reference to be present, only the elongation factor.
    FASTQ_ALIGN_BWAALN_ELONGATED( ch_fastq_reads, ch_elongated_reference )
    ch_versions = ch_versions.mix( FASTQ_ALIGN_BWAALN_ELONGATED.out.versions.first() )

    ch_ref_for_realignsamfile = ch_reference
                                .join( ch_elongated_chr_list )
                                .map {
                                    meta, index, reference, elongated_chr_list ->
                                    [ meta, reference, elongated_chr_list ]
                                }
                                .map {
                                    // Prepend a new meta that contains the meta.reference value as the new_meta.reference attribute
                                    addNewMetaFromAttributes( it, "id" , "reference" , false )
                                }

    ch_input_for_realignsamfile = FASTQ_ALIGN_BWAALN_ELONGATED.out.bam
                                .map{
                                    // create meta consistent with rest of MAP workflow
                                    meta, bam ->
                                        def new_meta = meta + [ reference: meta.id_index ]
                                    [ new_meta, bam ]
                                }
                                .map {
                                    // Prepend a new meta that contains the meta.reference value as the new_meta.reference attribute
                                    addNewMetaFromAttributes( it, "reference" , "reference" , false )
                                }
                                .combine( ch_ref_for_realignsamfile, by: 0 )
                                .multiMap {
                                    ignore_me, meta, bam, ref_meta, ref_fasta, elongated_chr_list ->
                                    bam:      [ meta, bam ]
                                    fasta:    [ ref_meta, ref_fasta ]
                                    chr_list: [ ref_meta, elongated_chr_list ]
                                }

    CIRCULARMAPPER_REALIGNSAMFILE( ch_input_for_realignsamfile.bam, ch_input_for_realignsamfile.fasta, [ [], val_elongation_factor ], ch_input_for_realignsamfile.chr_list )
    ch_versions       = ch_versions.mix( CIRCULARMAPPER_REALIGNSAMFILE.out.versions.first() )
    ch_realigned_bams = CIRCULARMAPPER_REALIGNSAMFILE.out.bam

    SAMTOOLS_INDEX_REALIGNED( ch_realigned_bams )
    ch_versions       = ch_versions.mix( SAMTOOLS_INDEX_REALIGNED.out.versions.first() )
    ch_realigned_bais = params.fasta_largeref ? SAMTOOLS_INDEX_REALIGNED.out.csi : SAMTOOLS_INDEX_REALIGNED.out.bai

    emit:
    bam      = ch_realigned_bams // [ meta, bam ]
    bai      = ch_realigned_bais // [ meta, bai/csi ]
    versions = ch_versions
    mqc      = ch_multiqc_files
}