1. My new data analysis pipeline code

    First, I write a recipe file, 'metagenome.recipe', laying out my job description for, say, sequence trimming and assembly with Velvet:

    fasta_file soil-data.fa
    qc_filter min_length=50 remove_Ns=true
    graph_filter min_length=400
    velvet_assemble k=33 min_length=1000 scaffolding=True

    Then I specify machine parameters, e.g. 'bigmem.conf':

    n_threads …
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