README.md

Documentation

This wrapper assesses an assembly using Quast.

Required input:

• fastq: the input fastq files.
• assembly: the input assembly fasta file.

Required output::

• output: Any empty filename. The path defines the quast output directory.

Required parameters:

• preset: preset for application (single, pacbio, nanopore). Ignored if fastq are paired-end.
• reference: reference genome fasta file.
• annotation: file with genomic feature coordinates in the reference (GFF, BED, NCBI or TXT).
• options: a list of valid Quast options.

Log:

• a log file generated by quast is created.

Configuration

##############################################################################
# Quast
#
# :Parameters:
#
# preset: preset for application (single, pacbio, nanopore). Ignored if fastq are paired-end.
# reference: reference genome fasta file.
# annotation: file with genomic feature coordinates in the reference (GFF, BED, NCBI or TXT).
# options: a list of valid quast.py options.
#
quast:
    preset: pacbio
    reference: path_to/knowned_ref.fa
    annotation: path_to/knowed_ref.gff
    options: "--fungus"
    threads: 4

Example

rule quast:
    input:
        fastq="data/raw.fastq.gz",
        assembly="assembly/contigs.fasta"
    output: "quast/quast.done"
    params:
        preset=config["quast"]["preset"],
        reference=config["quast"]["reference"],
        annotation=config["quast"]["annotation"],
        options=config["quast"]["options"],
    log:
        "logs/quast.log"
    threads:
        config["quast"]["threads"]
    wrapper:
        "main/wrappers/quast"