.. _`bio/quast`:

QUAST
=====


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/quast?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/quast

Quality Assessment Tool for Genome Assemblies


**URL**: https://github.com/ablab/quast

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule quast:
        input:
            fasta="genome.fasta",
            ref="genome.fasta",
            #gff="annotations.gff",
            #pe1="reads_R1.fastq",
            #pe2="reads_R2.fastq",
            #pe12="reads.fastq",
            #mp1="matereads_R1.fastq",
            #mp2="matereads_R2.fastq",
            #mp12="matereads.fastq",
            #single="single.fastq",
            #pacbio="pacbio.fas",
            #nanopore="nanopore.fastq",
            #ref_bam="ref.bam",
            #ref_sam="ref.sam",
            #bam=["s1.bam","s2.bam"],
            #sam=["s1.sam","s2.sam"],
            #sv_bedpe="sv.bed",
        output:
            multiext("{sample}/report.", "html", "tex", "txt", "pdf", "tsv"),
            multiext("{sample}/transposed_report.", "tex", "txt", "tsv"),
            multiext(
                "{sample}/basic_stats/",
                "cumulative_plot.pdf",
                "GC_content_plot.pdf",
                "gc.icarus.txt",
                "genome_GC_content_plot.pdf",
                "NGx_plot.pdf",
                "Nx_plot.pdf",
            ),
            multiext(
                "{sample}/contigs_reports/",
                "all_alignments_genome.tsv",
                "contigs_report_genome.mis_contigs.info",
                "contigs_report_genome.stderr",
                "contigs_report_genome.stdout",
            ),
            "{sample}/contigs_reports/minimap_output/genome.coords_tmp",
            "{sample}/icarus.html",
            "{sample}/icarus_viewers/contig_size_viewer.html",
            "{sample}/quast.log",
        log:
            "logs/{sample}.quast.log",
        params:
            extra="--min-contig 5 --min-identity 95.0",
        wrapper:
            "v3.0.1/bio/quast"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Notes
-----

* The `extra` param allows for additional program arguments.


Software dependencies
---------------------

* ``quast=5.2.0``

Input/Output
------------
**Input:**

* Sequences in FASTA format
* Reference genome (optional)
* GFF (optional)
* Paired end read (optional)
* Mate-pair reads (optional)
* Unpaired reads (optional)
* PacBio SMRT reads (optional)
* Oxford Nanopore reads (optional)
* Mapped reads against the reference in SAM/BAM (optional)
* Mapped reads against each of the assemblies in SAM/BAM (same order; optional)
* Structural variants in BEDPE (optional)

**Output:**

* Assessment summary in plain text format
* Tab-separated version of the summary
* LaTeX version of the summary
* Icarus main menu with links to interactive viewers
* PDF report of all plots combined with all tables
* HTML version of the report with interactive plots inside
* Report on misassemblies
* Report on unaligned and partially unaligned contigs
* Report on k-mer-based metrics
* Report on mapped reads statistics.




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell


    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)


    ref = snakemake.input.get("ref", "")
    if ref:
        ref = f"-r {ref}"

    gff = snakemake.input.get("gff", "")
    if gff:
        gff = f"--features {gff}"

    pe1 = snakemake.input.get("pe1", "")
    if pe1:
        pe1 = f"--pe1 {pe1}"
    pe2 = snakemake.input.get("pe2", "")
    if pe2:
        pe2 = f"--pe2 {pe2}"
    pe12 = snakemake.input.get("pe12", "")
    if pe12:
        pe12 = f"--pe12 {pe12}"
    mp1 = snakemake.input.get("mp1", "")
    if mp1:
        mp1 = f"--mp1 {mp1}"
    mp2 = snakemake.input.get("mp2", "")
    if mp2:
        mp2 = f"--mp2 {mp2}"
    mp12 = snakemake.input.get("mp12", "")
    if mp12:
        mp12 = f"--mp12 {mp12}"
    single = snakemake.input.get("single", "")
    if single:
        single = f"--single {single}"
    pacbio = snakemake.input.get("pacbio", "")
    if pacbio:
        pacbio = f"--pacbio {pacbio}"
    nanopore = snakemake.input.get("nanopore", "")
    if nanopore:
        nanopore = f"--nanopore {nanopore}"
    ref_bam = snakemake.input.get("ref_bam", "")
    if ref_bam:
        ref_bam = f"--ref-bam {ref_bam}"
    ref_sam = snakemake.input.get("ref_sam", "")
    if ref_sam:
        ref_sam = f"--ref-sam {ref_sam}"
    bam = snakemake.input.get("bam", "")
    if bam:
        if isinstance(bam, list):
            bam = ",".join(bam)
        bam = f"--bam {bam}"
    sam = snakemake.input.get("sam", "")
    if sam:
        if isinstance(sam, list):
            sam = ",".join(sam)
        sam = f"--sam {sam}"
    sv_bedpe = snakemake.input.get("sv_bedpe", "")
    if sv_bedpe:
        sv_bedpe = f"--sv-bedpe {sv_bedpe}"


    output_dir = os.path.commonpath(snakemake.output)


    shell(
        "quast --threads {snakemake.threads} {ref} {gff} {pe1} {pe2} {pe12} {mp1} {mp2} {mp12} {single} {pacbio} {nanopore} {ref_bam} {ref_sam} {bam} {sam} {sv_bedpe} {extra} -o {output_dir} {snakemake.input.fasta} {log}"
    )


.. |nl| raw:: html

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