mirror of
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69 lines
2.6 KiB
Text
69 lines
2.6 KiB
Text
/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running full-size tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a full size pipeline test.
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Use as follows:
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nextflow run nf-core/taxprofiler -profile test_full,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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params {
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config_profile_name = 'Full test profile'
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config_profile_description = 'Full test dataset to check pipeline function'
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// Input data for full size test
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input = 'https://github.com/nf-core/test-datasets/raw/taxprofiler/samplesheet_full.csv'
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databases = 'https://github.com/nf-core/test-datasets/raw/taxprofiler/database_full.csv'
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// Genome references
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hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz'
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save_preprocessed_reads = false
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perform_shortread_qc = true
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shortread_qc_mergepairs = true
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perform_shortread_complexityfilter = false
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save_complexityfiltered_reads = false
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perform_longread_qc = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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save_hostremoval_index = false
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save_hostremoval_bam = false
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save_hostremoval_unmapped = false
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perform_runmerging = true
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save_runmerged_reads = false
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run_centrifuge = true
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centrifuge_save_reads = false
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run_diamond = true
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run_kaiju = true
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run_kraken2 = true
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kraken2_save_reads = false
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kraken2_save_readclassification = false
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kraken2_save_minimizers = false
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run_krakenuniq = true
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krakenuniq_save_reads = false
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krakenuniq_save_readclassifications = false
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run_bracken = true
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run_malt = true
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malt_save_reads = false
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malt_generate_megansummary = true
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run_metaphlan3 = true
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run_motus = true
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motus_save_mgc_read_counts = true
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run_profile_standardisation = true
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run_krona = true
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}
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cleanup = true
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