mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 12:28:17 +00:00
61 lines
1.8 KiB
Text
61 lines
1.8 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { LIMA } from '../../../modules/lima/main.nf' addParams( options: [args: '--isoseq --peek-guess', suffix: ".fl"] )
|
||
|
|
|
||
|
|
workflow test_lima_bam {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test' ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['pacbio']['ccs'], checkIfExists: true),
|
||
|
|
]
|
||
|
|
primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
|
||
|
|
|
||
|
|
LIMA ( input, primers )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_lima_fa {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test' ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'], checkIfExists: true),
|
||
|
|
]
|
||
|
|
primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
|
||
|
|
|
||
|
|
LIMA ( input, primers )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_lima_fa_gz {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test' ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], checkIfExists: true),
|
||
|
|
]
|
||
|
|
primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
|
||
|
|
|
||
|
|
LIMA ( input, primers )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_lima_fq {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test' ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'], checkIfExists: true),
|
||
|
|
]
|
||
|
|
primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
|
||
|
|
|
||
|
|
LIMA ( input, primers )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_lima_fq_gz {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test' ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true),
|
||
|
|
]
|
||
|
|
primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
|
||
|
|
|
||
|
|
LIMA ( input, primers )
|
||
|
|
}
|