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27 lines
918 B
Text
Executable file
27 lines
918 B
Text
Executable file
#!/usr/bin/env nextflow
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nextflow.preview.dsl=2
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params.outdir = "." // gets set in the nextflow.config files (to './results/trim_galore')
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params.verbose = false
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params.trim_galore_args = ''
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// trim_galore_args are best passed into the workflow in the following manner, e.g.:
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// --trim_galore_args="--clip_r1 10 --clip_r2 15 -j 2"
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if (params.verbose){
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println ("[WORKFLOW] TRIM GALORE ARGS: " + params.trim_galore_args)
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}
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// TODO: check the output files in some way
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// include '../../../tests/functions/check_process_outputs.nf'
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include '../main.nf' // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters
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ch_read_files = Channel
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.fromFilePairs('../../../test-datasets/test*{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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TRIM_GALORE (ch_read_files, params.outdir, params.trim_galore_args, params.verbose)
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}
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