105 lines
2.4 KiB
Text
Executable file
105 lines
2.4 KiB
Text
Executable file
#!/usr/bin/env nextflow
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include { validateParameters; fromSamplesheet } from 'plugin/nf-validation'
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include { CLIQUESNV } from './modules/cliquesnv'
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include { EFETCH } from './modules/efetch'
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include { FASTERQ_DUMP } from './modules/fasterq_dump'
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include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/haplotypes'
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include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
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include { HAPLINK_SEQUENCES } from './modules/haplink/sequences'
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include { HAPLINK_VARIANTS } from './modules/haplink/variants'
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include { MINIMAP2 } from './modules/minimap2'
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include { NANOFILT } from './modules/nanofilt'
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include { QUASIRECOMB } from './modules/quasirecomb'
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include { SHORAH_AMPLICON } from './modules/shorah/amplicon'
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include { SHORAH_SHOTGUN } from './modules/shorah/shotgun'
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include { VIQUAS } from './modules/viquas'
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workflow {
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validateParameters()
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Channel
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.fromSamplesheet("input")
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.set { ch_sras }
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FASTERQ_DUMP( ch_sras )
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FASTERQ_DUMP
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.out
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.set { ch_input }
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EFETCH("${params.reference}")
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EFETCH
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.out
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.set { ch_reference }
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NANOFILT( ch_input )
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NANOFILT
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.out
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.set { ch_reads }
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MINIMAP2( ch_reads, ch_reference )
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MINIMAP2
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.out
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.set { ch_alignments }
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CLIQUESNV(
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ch_alignments,
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'snv-pacbio'
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)
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HAPLINK_VARIANTS( ch_alignments, ch_reference )
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HAPLINK_VARIANTS
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.out
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.set { ch_variants }
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ch_alignments
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.join( ch_variants )
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.set { ch_haplotype_calling }
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HAPLINK_RAW_HAPLOTYPES(
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ch_haplotype_calling,
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ch_reference
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)
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HAPLINK_RAW_HAPLOTYPES
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.out
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.map{ [ it[0], 'HAPLINK_RAW_HAPLOTYPES', it[1] ] }
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.set{ ch_raw_haplotypes }
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HAPLINK_ML_HAPLOTYPES(
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ch_haplotype_calling,
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ch_reference
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)
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HAPLINK_ML_HAPLOTYPES
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.out
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.map{ [ it[0], 'HAPLINK_ML_HAPLOTYPES', it[1] ] }
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.set{ ch_ml_haplotypes }
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ch_raw_haplotypes
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.mix(ch_ml_haplotypes)
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.set{ ch_all_haplotypes }
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HAPLINK_SEQUENCES(
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ch_all_haplotypes,
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ch_reference
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)
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QUASIRECOMB( ch_alignments )
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SHORAH_AMPLICON(
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ch_alignments,
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ch_reference
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)
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SHORAH_SHOTGUN(
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ch_alignments,
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ch_reference
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)
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VIQUAS(
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ch_alignments,
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ch_reference
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)
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}
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