mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
35 lines
917 B
Text
35 lines
917 B
Text
|
#!/usr/bin/env nextflow
|
||
|
|
nextflow.preview.dsl=2
|
||
|
|
|
||
|
|
params.outdir = "."
|
||
|
|
params.genome = ""
|
||
|
|
params.hisat2_args = ''
|
||
|
|
// HISAT2 arguments should be supplied in the following format to work:
|
||
|
|
// --hisat2_args="--score-min L,0,-0.8"
|
||
|
|
|
||
|
|
params.verbose = false
|
||
|
|
|
||
|
|
if (params.verbose){
|
||
|
|
println ("[WORKFLOW] HISAT2 ARGS ARE: " + params.hisat2_args)
|
||
|
|
}
|
||
|
|
// for other genomes this needs to be handled somehow to return all possible genomes
|
||
|
|
genomeValues = ["name" : params.genome]
|
||
|
|
genomeValues["hisat2"] = "/bi/home/fkrueger/VersionControl/nf-core-modules/test-datasets/indices/hisat2/E_coli/${params.genome}";
|
||
|
|
|
||
|
|
include '../main.nf' params(genome: genomeValues)
|
||
|
|
|
||
|
|
ch_read_files = Channel
|
||
|
|
.fromFilePairs('../../../test-datasets/Ecoli*{1,2}.fastq.gz',size:-1)
|
||
|
|
// .view() // to check whether the input channel works
|
||
|
|
|
||
|
|
workflow {
|
||
|
|
|
||
|
|
main:
|
||
|
|
HISAT2(ch_read_files, params.outdir, params.hisat2_args, params.verbose)
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
|