2022-12-01 09:37:14 +00:00
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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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//
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// Separate test as KrakenUniq database can sometimes be too big for GHA
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//
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params {
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config_profile_name = 'Test profile'
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2022-12-01 11:53:34 +00:00
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config_profile_description = 'Minimal test to check KrakenUniq function'
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2022-12-01 09:37:14 +00:00
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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_krakenuniq.csv'
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perform_shortread_qc = true
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perform_longread_qc = true
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shortread_qc_mergepairs = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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perform_runmerging = true
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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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2022-12-01 12:46:57 +00:00
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run_kaiju = false
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run_kraken2 = false
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2022-12-01 09:37:14 +00:00
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run_bracken = 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_krakenuniq = true
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run_motus = false
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run_krona = true
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krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
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malt_save_reads = true
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kraken2_save_reads = true
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centrifuge_save_reads = true
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diamond_save_reads = true
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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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withName: MEGAN_RMA2INFO_TSV {
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maxForks = 1
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}
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withName: MEGAN_RMA2INFO_KRONA {
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maxForks = 1
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}
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withName: 'EIDO_VALIDATE' {
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ext.args = '--st-index sample'
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}
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withName: 'EIDO_CONVERT' {
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ext.args = '--st-index sample'
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}
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}
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