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30 lines
795 B
Text
Executable file
30 lines
795 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.fastq_screen_args = ''
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// fastq_screen_args are best passed in to the workflow in the following manner:
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// --fastq_screen_args="--subset 200000 --force"
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params.verbose = false
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if (params.verbose){
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println ("[WORKFLOW] FASTQ SCREEN ARGS ARE: " + params.fastq_screen_args)
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}
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// TODO: include '../../../tests/functions/check_process_outputs.nf'
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include '../main.nf'
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// Define input channels
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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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// Run the workflow
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workflow {
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main:
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FASTQ_SCREEN(ch_read_files, params.outdir, params.fastq_screen_args, params.verbose)
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// TODO .check_output()
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}
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