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cnvpytor_complete.nf
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cnvpytor_complete.nf
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include { CNVPYTOR_IMPORTREADDEPTH } from "../../modules/nf-core/cnvpytor/importreaddepth"
include { CNVPYTOR_HISTOGRAM } from "../../modules/nf-core/cnvpytor/histogram"
include { CNVPYTOR_PARTITION } from "../../modules/nf-core/cnvpytor/partition"
include { CNVPYTOR_VIEW } from "../../modules/nf-core/cnvpytor/view"
include { CNVPYTOR_VIEW as CNVPYTOR_VIEW_TSV_FLTR } from "../../modules/local/cnvpytor/view"
workflow CNVPYTOR_COMPLETE {
take:
bam_bai // channel: [ val(meta), path(bam), path(bai) ]
cnvpytor_genome_conf
cnvpytor_genome_gc_ch
main:
ch_versions = Channel.empty()
CNVPYTOR_IMPORTREADDEPTH(
bam_bai,
cnvpytor_genome_conf,
cnvpytor_genome_gc_ch
)
ch_versions = ch_versions.mix(CNVPYTOR_IMPORTREADDEPTH.out.versions.first())
CNVPYTOR_HISTOGRAM(
CNVPYTOR_IMPORTREADDEPTH.out.pytor
)
ch_versions = ch_versions.mix(CNVPYTOR_HISTOGRAM.out.versions.first())
CNVPYTOR_PARTITION(
CNVPYTOR_HISTOGRAM.out.pytor
)
ch_versions = ch_versions.mix(CNVPYTOR_PARTITION.out.versions.first())
CNVPYTOR_VIEW(
CNVPYTOR_PARTITION.out.pytor
)
ch_versions = ch_versions.mix(CNVPYTOR_VIEW.out.versions.first())
CNVPYTOR_VIEW_TSV_FLTR(
CNVPYTOR_PARTITION.out.pytor
)
ch_versions = ch_versions.mix(CNVPYTOR_VIEW_TSV_FLTR.out.versions.first())
emit:
versions = ch_versions // channel: [ versions.yml ]
}