nf-core_modules/tools/hisat2/test/main.nf
2020-03-20 11:04:25 +00:00

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#!/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)
}