refactor: Move EFETCH module to its own file

This commit is contained in:
Thomas A. Christensen II 2023-09-23 15:34:27 -05:00
parent 2c755dcd4f
commit 18875ae1a6
Signed by: millironx
GPG key ID: 09335146883990B9
2 changed files with 21 additions and 21 deletions

22
main.nf
View file

@ -1,5 +1,6 @@
#!/usr/bin/env nextflow
include { EFETCH } from './modules/efetch'
include { HAPLINK_VARIANTS } from './modules/haplink/variants'
include { VIQUAS } from './modules/viquas'
@ -68,27 +69,6 @@ workflow {
)
}
process EFETCH {
cpus 1
memory '256.MB'
container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
publishDir "results", mode: 'copy'
output:
path 'idv4.fasta'
script:
"""
esearch \\
-db nucleotide \\
-query "NC_036618.1" \\
| efetch \\
-format fasta \\
> idv4.fasta
"""
}
process NANOFILT {
cpus 1
memory '8.GB'

20
modules/efetch/main.nf Normal file
View file

@ -0,0 +1,20 @@
process EFETCH {
cpus 1
memory '256.MB'
container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
publishDir "results", mode: 'copy'
output:
path 'idv4.fasta'
script:
"""
esearch \\
-db nucleotide \\
-query "NC_036618.1" \\
| efetch \\
-format fasta \\
> idv4.fasta
"""
}