Olamide Isreal
8dd0ef8d6a
Some checks failed
Tests / build (ubuntu-latest, 3.10) (push) Has been cancelled
Tests / build (ubuntu-latest, 3.11) (push) Has been cancelled
Tests / build (ubuntu-latest, 3.12) (push) Has been cancelled
Tests / build (ubuntu-latest, 3.8) (push) Has been cancelled
Tests / build (ubuntu-latest, 3.9) (push) Has been cancelled
Tests / build (windows-latest, 3.10) (push) Has been cancelled
Tests / build (windows-latest, 3.11) (push) Has been cancelled
Tests / build (windows-latest, 3.12) (push) Has been cancelled
Tests / build (windows-latest, 3.8) (push) Has been cancelled
Tests / build (windows-latest, 3.9) (push) Has been cancelled
Tests / static_type_check (push) Has been cancelled
- Update container reference to harbor.cluster.omic.ai/omic/propka:latest - Add k8s profile to nextflow.config matching reference tool pattern - Update params.json with s3://omic/eureka/propka/ paths - Add stageInMode 'copy' to process definition - Set params defaults to null for WES compatibility
32 lines
579 B
Plaintext
32 lines
579 B
Plaintext
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl=2
|
|
|
|
params.pdb = null
|
|
params.outdir = null
|
|
params.ph = 7.0
|
|
params.options = ""
|
|
|
|
process PROPKA {
|
|
container 'harbor.cluster.omic.ai/omic/propka:latest'
|
|
publishDir params.outdir, mode: 'copy'
|
|
stageInMode 'copy'
|
|
|
|
input:
|
|
path pdb
|
|
|
|
output:
|
|
path "${pdb.baseName}.pka", emit: pka_file
|
|
path "run.log"
|
|
|
|
script:
|
|
"""
|
|
propka3 ${params.options} --pH ${params.ph} ${pdb} 2>&1 | tee run.log
|
|
"""
|
|
}
|
|
|
|
workflow {
|
|
pdb_files = Channel.fromPath(params.pdb)
|
|
PROPKA(pdb_files)
|
|
}
|