Clair3 variant caller

[bgruening]

trafficstars

That seems to be an interesting ONT variant caller: https://github.com/nanoporetech/Clair3

[mira-miracoli]

I would like to try it :)

[pvanheus]

I made a very small start on this:

<tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy0" profile="21.09">
    <macros>
        <token name="@TOOL_VERSION@">0.1.10</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">clair3</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $ref_source.source == "history"
            ln -s '$ref_source.ref_fasta' reference.fasta &&
        #elif $ref_source.source == "builtin"
            ln -s '$ref_source.ref_fasta_builtin.path' reference.fasta &&
        #end if
        BIN_PATH=\$(dirname \$(which run_clair3.sh))
        #import os
        #if os.getenv('BIN_DIR') is not None
            #set $model_prefix = os.environ.get('BIN_PATH') + '/models/'
        #end if
        
        run_clair3.sh
            --bam_fn='$bam_input'
            --ref_fn=reference.fasta
            --model_path='$model_prefix/$model'
            --plaform='ont'
            --output='clair3_output'
            --threads=\${GALAXY_SLOTS:-1}

    ]]></command>
    <inputs>
        <conditional name="ref_source">
            <param type="select" label="Reference genome source" name="source">
                <option value="history" selected="true">History</option>
                <option value="builtin">Built-in</option>
            </param>
            <when value="history">
                <param type="data" format="fasta" name="ref_fasta" label="Reference genome" />
            </when>
            <when value="builtin">
                <param type="select" name="ref_fasta_builtin" label="Reference genome">
                    <options from_data_table="all_fasta" />
                </param>
            </when>
        </conditional>        
    </inputs>
    <outputs>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>

[gallardoalba]

Closed in https://github.com/galaxyproject/tools-iuc/pull/4392