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66 lines
1.8 KiB
Text
Executable file
66 lines
1.8 KiB
Text
Executable file
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { TRIMGALORE } from '../main.nf'
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/*
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* Test with single-end data
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*/
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workflow test_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
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TRIMGALORE ( input, [ publish_dir:'test_single_end' ] )
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}
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/*
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* Test with paired-end data
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*/
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workflow test_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
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file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
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TRIMGALORE ( input, [ publish_dir:'test_paired_end' ] )
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}
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workflow {
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test_single_end()
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test_paired_end()
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}
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// #!/usr/bin/env nextflow
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// nextflow.preview.dsl=2
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//
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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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//
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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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//
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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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//
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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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//
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// workflow {
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//
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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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// }
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