/*
 * Run SAMtools stats, flagstat and idxstats
 */

params.options = [:]

include { SAMTOOLS_STATS    } from '../../modules/nf-core/modules/samtools/stats/main'    addParams( options: params.options )
include { SAMTOOLS_IDXSTATS } from '../../modules/nf-core/modules/samtools/idxstats/main' addParams( options: params.options )
include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/modules/samtools/flagstat/main' addParams( options: params.options )

workflow BAM_STATS_SAMTOOLS {
    take:
    ch_bam_bai // channel: [ val(meta), [ bam ], [bai] ]

    main:
    ch_versions = Channel.empty()

    SAMTOOLS_STATS    ( ch_bam_bai )
    ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions)

    SAMTOOLS_FLAGSTAT ( ch_bam_bai )
    ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions)

    SAMTOOLS_IDXSTATS ( ch_bam_bai )
    ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions)

    emit:
    stats    = SAMTOOLS_STATS.out.stats       // channel: [ val(meta), [ stats ] ]
    flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), [ flagstat ] ]
    idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
    versions = ch_versions                    // channel: [ versions.yml ]
}
