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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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