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now with test data

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This commit is contained in:
veitveit 2022-02-07 11:20:25 +01:00
parent 273d44f1f7
commit 8f9f452a62
3 changed files with 14 additions and 3 deletions
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11
tests/config/test_data.config
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@ -382,5 +382,16 @@ params {
} }
} }
'proteomics' {
'msspectra' {
ups_file1 = "{test_data_dir}/proteomics/msspectra/OVEMB150205_12.raw"
ups_file2 = "{test_data_dir}/proteomics/msspectra/OVEMB150205_14.raw"
}
'database' {
yeast_ups = "{test_data_dir}/proteomics/database/yeast_UPS.fasta"
}
'parameter' {
maxquant = "{test_data_dir}/proteomics/parameter/mqpar.xml"
}
} }
} }

4
tests/modules/maxquant/lfq/main.nf
View file

@ -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.fasta, checkIfExists: true), file(params.paramfile, checkIfExists: true) file(params_test_data['proteomics']['database']['yeast_ups']), checkIfExists: true), file(params_test_data['proteomics']['parameter']['maxquant'] , checkIfExists: true)
] ]
rawfiles = [file('https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/OVEMB150205_12.raw') , file('https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/OVEMB150205_14.raw') ] 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/test.yml
View file

@ -1,7 +1,7 @@
## TODO nf-core: Please run the following command to build this file: ## TODO nf-core: Please run the following command to build this file:
# nf-core modules create-test-yml maxquant/lfq # 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 --paramfile 'https://raw.githubusercontent.com/wombat-p/DSL2-data/master/nf-core-modules/test_data/maxquant/mqpar.xml' --fasta 'https://raw.githubusercontent.com/wombat-p/MaxQuant-Workflow/dev/data/yeast_UPS.fasta' -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