refactor: Move SHORAH_SHOTGUN to its own file
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2 changed files with 23 additions and 23 deletions
24
main.nf
24
main.nf
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@ -5,6 +5,7 @@ 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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include { SHORAH_AMPLICON } from './modules/shorah/amplicon'
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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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include { VIQUAS } from './modules/viquas'
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workflow {
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workflow {
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@ -72,29 +73,6 @@ workflow {
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)
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)
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}
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}
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process SHORAH_SHOTGUN {
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label 'process_high'
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container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
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input:
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tuple val(prefix), path(bam)
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path(reference)
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output:
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tuple val(prefix), path("*.vcf")
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tuple val(prefix), path("*support.fas")
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publishDir "results/shorah-shotgun", mode: 'copy'
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script:
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"""
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shorah shotgun \\
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-t ${task.cpus} \\
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-f ${reference} \\
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-b ${bam} \\
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"""
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}
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process HAPLINK_RAW_HAPLOTYPES {
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process HAPLINK_RAW_HAPLOTYPES {
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cpus 2
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cpus 2
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memory '12.GB'
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memory '12.GB'
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22
modules/shorah/shotgun/main.nf
Normal file
22
modules/shorah/shotgun/main.nf
Normal file
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@ -0,0 +1,22 @@
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process SHORAH_SHOTGUN {
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label 'process_high'
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container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
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input:
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tuple val(prefix), path(bam)
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path(reference)
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output:
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tuple val(prefix), path("*.vcf")
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tuple val(prefix), path("*support.fas")
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publishDir "results/shorah-shotgun", mode: 'copy'
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script:
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"""
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shorah shotgun \\
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-t ${task.cpus} \\
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-f ${reference} \\
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-b ${bam} \\
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"""
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}
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