nf-core_modules/software/bowtie2/test/main.nf
2020-07-11 14:27:21 +02:00

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#!/usr/bin/env nextflow
nextflow.preview.dsl=2
params.outdir = "."
params.genome = ""
params.bowtie2_args = ''
// Bowtie2 arguments should be supplied in the following format to work:
// --bowtie2_args="--score-min L,0,-0.8"
params.verbose = false
if (params.verbose){
println ("[WORKFLOW] BOWTIE2 ARGS: " + params.bowtie2_args)
}
// for other genomes this needs to be handled somehow to return all possible genomes
genomeValues = ["name" : params.genome]
genomeValues["bowtie2"] = "/bi/home/fkrueger/VersionControl/nf-core-modules/test-datasets/indices/bowtie2/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:
BOWTIE2(ch_read_files, params.outdir, params.bowtie2_args, params.verbose)
}