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