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Update tests

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drpatelh 2020-08-07 12:18:53 +01:00
parent 2c0f552908
commit 30256d8e81
1 changed files with 57 additions and 18 deletions
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75
software/trimgalore/test/main.nf
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@ -1,27 +1,66 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
nextflow.preview.dsl=2
params.outdir = "." // gets set in the nextflow.config files (to './results/trim_galore') nextflow.enable.dsl = 2
params.verbose = false
params.trim_galore_args = ''
// trim_galore_args are best passed into the workflow in the following manner, e.g.:
// --trim_galore_args="--clip_r1 10 --clip_r2 15 -j 2"
if (params.verbose){ include { TRIMGALORE } from '../main.nf'
println ("[WORKFLOW] TRIM GALORE ARGS: " + params.trim_galore_args)
/*
* Test with single-end data
*/
workflow test_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE ( input, [ publish_dir:'test_single_end' ] )
} }
// TODO: check the output files in some way /*
// include '../../../tests/functions/check_process_outputs.nf' * Test with paired-end data
include '../main.nf' // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters */
workflow test_paired_end {
ch_read_files = Channel def input = []
.fromFilePairs('../../../test-datasets/test*{1,2}.fastq.gz',size:-1) input = [ [ id:'test', single_end:false ], // meta map
// .view() // to check whether the input channel works [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE ( input, [ publish_dir:'test_paired_end' ] )
}
workflow { workflow {
test_single_end()
main: test_paired_end()
TRIM_GALORE (ch_read_files, params.outdir, params.trim_galore_args, params.verbose)
} }
// #!/usr/bin/env nextflow
// nextflow.preview.dsl=2
//
// params.outdir = "." // gets set in the nextflow.config files (to './results/trim_galore')
// params.verbose = false
// params.trim_galore_args = ''
// // trim_galore_args are best passed into the workflow in the following manner, e.g.:
// // --trim_galore_args="--clip_r1 10 --clip_r2 15 -j 2"
//
// if (params.verbose){
// println ("[WORKFLOW] TRIM GALORE ARGS: " + params.trim_galore_args)
// }
//
// // TODO: check the output files in some way
// // include '../../../tests/functions/check_process_outputs.nf'
// include '../main.nf' // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters
//
// ch_read_files = Channel
// .fromFilePairs('../../../test-datasets/test*{1,2}.fastq.gz',size:-1)
// // .view() // to check whether the input channel works
//
// workflow {
//
// main:
// TRIM_GALORE (ch_read_files, params.outdir, params.trim_galore_args, params.verbose)
//
// }