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corrected typos

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This commit is contained in:
veitveit 2022-02-07 13:07:16 +01:00
parent 7df2fb74a3
commit 5b9313c2c5
4 changed files with 9 additions and 10 deletions
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9
tests/config/test_data.config
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@ -384,14 +384,15 @@ params {
} }
'proteomics' { 'proteomics' {
'msspectra' { 'msspectra' {
ups_file1 = "{test_data_dir}/proteomics/msspectra/OVEMB150205_12.raw" ups_file1 = "${test_data_dir}/proteomics/msspectra/OVEMB150205_12.raw"
ups_file2 = "{test_data_dir}/proteomics/msspectra/OVEMB150205_14.raw" ups_file2 = "${test_data_dir}/proteomics/msspectra/OVEMB150205_14.raw"
} }
'database' { 'database' {
yeast_ups = "{test_data_dir}/proteomics/database/yeast_UPS.fasta" yeast_ups = "${test_data_dir}/proteomics/database/yeast_UPS.fasta"
} }
'parameter' { 'parameter' {
maxquant = "{test_data_dir}/proteomics/parameter/mqpar.xml" maxquant = "${test_data_dir}/proteomics/parameter/mqpar.xml"
}
} }
} }
} }

4
tests/modules/maxquant/lfq/main.nf
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@ -7,11 +7,11 @@ include { MAXQUANT_LFQ } from '../../../../modules/maxquant/lfq/main.nf' addPara
workflow test_maxquant_lfq { workflow test_maxquant_lfq {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params_test_data['proteomics']['database']['yeast_ups']), checkIfExists: true), file(params_test_data['proteomics']['parameter']['maxquant'] , checkIfExists: true) file(params.test_data['proteomics']['database']['yeast_ups'], checkIfExists: true), file(params.test_data['proteomics']['parameter']['maxquant'] , checkIfExists: true)
] ]
rawfiles = [file(params_test_data['proteomics']['msspectra']['ups_file1']) , file(params_test_data['proteomics']['msspectra']['ups_file2']) ] rawfiles = [file(params.test_data['proteomics']['msspectra']['ups_file1']) , file(params.test_data['proteomics']['msspectra']['ups_file2'])]
MAXQUANT_LFQ ( input, rawfiles.collect() ) MAXQUANT_LFQ ( input, rawfiles.collect() )
} }

2
tests/modules/maxquant/lfq/nextflow.config
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@ -2,4 +2,4 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
} }

4
tests/modules/maxquant/lfq/test.yml
View file

@ -1,7 +1,5 @@
## TODO nf-core: Please run the following command to build this file:
# nf-core modules create-test-yml maxquant/lfq
- name: maxquant lfq - name: maxquant lfq
command: nextflow run ./tests/modules/maxquant/lfq -entry test_maxquant_lfq -c tests/config/nextflow.config command: nextflow run ./tests/modules/maxquant/lfq -entry test_maxquant_lfq -c tests/config/nextflow.config
tags: tags:
- maxquant - maxquant
- maxquant/lfq - maxquant/lfq