refactor: Move HAPLINK_SEQUENCES module to its own file
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2 changed files with 24 additions and 24 deletions
25
main.nf
25
main.nf
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@ -3,6 +3,7 @@
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include { EFETCH } from './modules/efetch'
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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_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_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 { HAPLINK_VARIANTS } from './modules/haplink/variants'
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include { MINIMAP2 } from './modules/minimap2'
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include { MINIMAP2 } from './modules/minimap2'
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include { NANOFILT } form './modules/nanofilt'
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include { NANOFILT } form './modules/nanofilt'
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@ -74,27 +75,3 @@ workflow {
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ch_reference
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ch_reference
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)
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)
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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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23
modules/haplink/sequences/main.nf
Normal file
23
modules/haplink/sequences/main.nf
Normal file
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@ -0,0 +1,23 @@
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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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