.. _`bio/salsa2`:

SALSA2
======


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/salsa2?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/salsa2

A tool to scaffold long read assemblies with Hi-C data


**URL**: https://github.com/marbl/SALSA

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule salsa2:
        input:
            fas="{sample}.fasta",
            fai="{sample}.fasta.fai",
            bed="{sample}.bed",
        output:
            agp="out/{sample}.agp",
            fas="out/{sample}.fas",
        log:
            "logs/salsa2/{sample}.log",
        params:
            enzyme="CTTAAG",  # optional
            extra="--clean yes",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.4/bio/salsa2"

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
---------------------

* ``salsa2=2.3``

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

* BED file
* FASTA file
* FASTA index file

**Output:**

* polished assembly (FASTA format)
* polished assembly (AGP format)




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

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


    import tempfile
    from snakemake.shell import shell


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


    enzyme = snakemake.params.get("enzyme", "")
    if enzyme:
        enzyme = f"--enzyme {enzyme}"

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


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "run_pipeline.py"
            " --assembly {snakemake.input.fas}"
            " --length {snakemake.input.fai}"
            " --bed {snakemake.input.bed}"
            " {enzyme}"
            " {gfa}"
            " {extra}"
            " --output {tmpdir}"
            " {log}"
        )

        if snakemake.output.get("agp"):
            shell("cat {tmpdir}/scaffolds_FINAL.agp > {snakemake.output.agp}")
        if snakemake.output.get("fas"):
            shell("cat {tmpdir}/scaffolds_FINAL.fasta > {snakemake.output.fas}")


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