refactor: Move SHORAH_SHOTGUN to its own file

This commit is contained in:
Thomas A. Christensen II 2023-09-23 16:12:40 -05:00
parent f6111f27c2
commit db0255c54a
Signed by: millironx
GPG key ID: 09335146883990B9
2 changed files with 23 additions and 23 deletions

24
main.nf
View file

@ -5,6 +5,7 @@ include { HAPLINK_VARIANTS } from './modules/haplink/variants'
include { MINIMAP2 } from './modules/minimap2'
include { NANOFILT } form './modules/nanofilt'
include { SHORAH_AMPLICON } from './modules/shorah/amplicon'
include { SHORAH_SHOTGUN } from './modules/shorah/shotgun'
include { VIQUAS } from './modules/viquas'
workflow {
@ -72,29 +73,6 @@ workflow {
)
}
process SHORAH_SHOTGUN {
label 'process_high'
container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
input:
tuple val(prefix), path(bam)
path(reference)
output:
tuple val(prefix), path("*.vcf")
tuple val(prefix), path("*support.fas")
publishDir "results/shorah-shotgun", mode: 'copy'
script:
"""
shorah shotgun \\
-t ${task.cpus} \\
-f ${reference} \\
-b ${bam} \\
"""
}
process HAPLINK_RAW_HAPLOTYPES {
cpus 2
memory '12.GB'

View file

@ -0,0 +1,22 @@
process SHORAH_SHOTGUN {
label 'process_high'
container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
input:
tuple val(prefix), path(bam)
path(reference)
output:
tuple val(prefix), path("*.vcf")
tuple val(prefix), path("*support.fas")
publishDir "results/shorah-shotgun", mode: 'copy'
script:
"""
shorah shotgun \\
-t ${task.cpus} \\
-f ${reference} \\
-b ${bam} \\
"""
}