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Merge pull request #111 from nf-core/minimal-test
Add test_nothing config profile for very minimal testing
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commit
22e03e73e3
2 changed files with 53 additions and 5 deletions
47
conf/test_nothing.config
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47
conf/test_nothing.config
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:
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nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others'
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '6.h'
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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_qc = false
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perform_longread_qc = false
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perform_shortread_complexityfilter = false
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perform_shortread_hostremoval = false
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perform_longread_hostremoval = false
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perform_runmerging = false
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hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = false
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run_kraken2 = false
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run_malt = false
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run_metaphlan3 = false
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run_centrifuge = false
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run_diamond = false
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run_motus = false
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}
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process {
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withName: MALT_RUN {
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maxForks = 1
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}
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}
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@ -204,11 +204,12 @@ profiles {
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podman.enabled = false
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shifter.enabled = false
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}
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test { includeConfig 'conf/test.config' }
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test_full { includeConfig 'conf/test_full.config' }
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test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
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test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
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test_motus { includeConfig 'conf/test_motus.config' }
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test { includeConfig 'conf/test.config' }
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test_full { includeConfig 'conf/test_full.config' }
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test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
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test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
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test_nothing { includeConfig 'conf/test_nothing.config' }
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test_motus { includeConfig 'conf/test_motus.config' }
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}
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// Load igenomes.config if required
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