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| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Nextflow config file for running minimal tests | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Defines input files and everything required to run a fast and simple pipeline test. | ||
| Use as follows: | ||
| nextflow run nf-core/ampliseq -profile test_sintax,<docker/singularity> --outdir <OUTDIR> | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
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| params { | ||
| config_profile_name = 'Test sintax profile' | ||
| config_profile_description = 'Minimal test dataset to check pipeline function when using sintax for taxonomy assignment' | ||
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| // Limit resources so that this can run on GitHub Actions | ||
| max_cpus = 2 | ||
| max_memory = '12.GB' | ||
| max_time = '6.h' | ||
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| // Input data | ||
| FW_primer = "CTTGGTCATTTAGAGGAAGTAA" | ||
| RV_primer = "TCCTGAGGGAAACTTCG" | ||
| input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_pacbio_ITS.tsv" | ||
| metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Metadata_pacbio_ITS.tsv" | ||
| pacbio = true | ||
| max_ee = 12 | ||
| cut_its = "its2" | ||
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| skip_dada_taxonomy = false | ||
| dada_ref_taxonomy = "unite-fungi" | ||
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| //this is to remove low abundance ASVs to reduce runtime of downstream processes | ||
| min_samples = 2 | ||
| min_frequency = 10 | ||
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| //produce average barplots | ||
| metadata_category_barplot = "var2,var3" | ||
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| //restrict ANCOM analysis to higher taxonomic levels | ||
| tax_agglom_max = 4 | ||
| ancom = true | ||
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| sbdiexport = true | ||
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| qiime_adonis_formula = "var2" | ||
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| diversity_rarefaction_depth = 500 | ||
| } |
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