100 lines
2.2 KiB
Text
Executable file
100 lines
2.2 KiB
Text
Executable file
#!/usr/bin/env nextflow
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include { EFETCH } from './modules/efetch'
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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_VARIANTS } from './modules/haplink/variants'
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include { MINIMAP2 } from './modules/minimap2'
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include { NANOFILT } form './modules/nanofilt'
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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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Channel
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.fromPath("*.fastq.gz")
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.map { file -> tuple(file.simpleName, file) }
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.set { ch_input }
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EFETCH('NC_036618.1')
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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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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], 'raw', 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], 'ml', 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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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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process HAPLINK_SEQUENCES {
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cpus 1
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memory '6.GB'
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input:
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tuple val(prefix), val(method), path(yaml)
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path reference
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output:
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tuple val(prefix), val(method), path("*.fasta")
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publishDir "results/${method}-haplotypes", mode: 'copy'
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script:
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"""
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export JULIA_NUM_THREADS=${task.cpus}
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haplink sequences \\
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"${reference}" \\
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"${yaml}" \\
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--prefix "${prefix}" \\
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> "${prefix}.fasta"
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"""
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}
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