feat: Add SHORAH_AMPLICON process

This commit is contained in:
Thomas A. Christensen II 2023-06-08 18:10:26 -05:00
parent 58b18cc2c9
commit feb051fc07
Signed by: millironx
GPG key ID: 09335146883990B9

23
main.nf
View file

@ -142,6 +142,29 @@ process MINIMAP2 {
"""
}
process SHORAH_AMPLICON {
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-amplicon", mode: 'copy'
script:
"""
shorah amplicon \\
-t ${task.cpus} \\
-f ${reference} \\
-b ${bam} \\
"""
}
process HAPLINK_VARIANTS {
cpus 2
memory '12.GB'