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refactor: Move HAPLINK_VARIANTS module to its own folder

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This commit is contained in:
Thomas A. Christensen II 2023-09-23 15:21:26 -05:00
parent a91632a883
commit 2829d51533
Signed by: millironx
GPG key ID: 09335146883990B9
2 changed files with 23 additions and 23 deletions
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24
main.nf
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@ -1,5 +1,6 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
include { HAPLINK_VARIANTS } from './modules/haplink/variants'
include { VIQUAS } from './modules/viquas' include { VIQUAS } from './modules/viquas'
workflow { workflow {
@ -195,29 +196,6 @@ process SHORAH_SHOTGUN {
""" """
} }
process HAPLINK_VARIANTS {
cpus 2
memory '12.GB'
input:
tuple val(prefix), path(bam), path(bai)
path reference
output:
tuple val(prefix), path("*.vcf")
publishDir "results", mode: 'copy'
script:
"""
export JULIA_NUM_THREADS=${task.cpus}
haplink variants \\
"${reference}" \\
"${bam}" \\
> "${prefix}.vcf"
"""
}
process HAPLINK_RAW_HAPLOTYPES { process HAPLINK_RAW_HAPLOTYPES {
cpus 2 cpus 2
memory '12.GB' memory '12.GB'

22
modules/haplink/variants/main.nf Normal file
View file

@ -0,0 +1,22 @@
process HAPLINK_VARIANTS {
cpus 2
memory '12.GB'
input:
tuple val(prefix), path(bam), path(bai)
path reference
output:
tuple val(prefix), path("*.vcf")
publishDir "results", mode: 'copy'
script:
"""
export JULIA_NUM_THREADS=${task.cpus}
haplink variants \\
"${reference}" \\
"${bam}" \\
> "${prefix}.vcf"
"""
}