Workflows and Tools

Available Workflows

To see the available workflows, run:

elvers examples/nema.yaml --print_workflows

You should see something like this:

####################  Available Eelpond Workflows  ####################

  default:
    get_data
    trimmomatic
    khmer
    trinity
    fastqc
    dammit
    salmon
    sourmash

  protein_assembly:
    get_data
    trimmomatic
    khmer
    plass
    pear
    fastqc
    paladin
    sourmash

  preprocess:
    get_data
    fastqc
    trimmomatic

  kmer_trim:
    get_data
    trimmomatic
    khmer

  assemble:
    get_data
    trimmomatic
    khmer
    trinity

  annotate:
    dammit

  quantify:
    get_data
    trimmomatic
    salmon

  diffexp:
    get_data
    trimmomatic
    salmon
    deseq2

  sourmash_compute:
    get_data
    trimmomatic
    khmer
    sourmash

  plass_assemble:
    get_data
    trimmomatic
    khmer
    plass

  paladin_map:
    get_data
    trimmomatic
    khmer
    plass
    pear
    paladin

  correct_reads:
    get_data
    trimmomatic
    rcorrector

Available Tools

To see the available integrated programs, run:

elvers examples/nema.yaml --print_rules

You should see something like this:

  ####################  Advanced usage: all available ruless  ####################

    get_data
    trimmomatic
    fastqc
    rcorrector
    khmer
    trinity
    salmon
    deseq2
    dammit
    sourmash
    get_reference
    plass
    pear
    paladin