FastaSplitter_conf.pm

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=pod
 
=head1 NAME
 
    Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::FastaSplitter_conf
 
=head1 SYNOPSIS
 
    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::FastaSplitter_conf -inputfile reference.fasta -chunks_dir reference_chunks
 
=head1 LICENSE
 
    See the NOTICE file distributed with this work for additional information
    regarding copyright ownership.
 
    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
    You may obtain a copy of the License at
 
         http://www.apache.org/licenses/LICENSE-2.0
 
    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and limitations under the License.
 
=head1 CONTACT
 
    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates
 
=cut
 
 
package Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::FastaSplitter_conf;
 
use strict;
use warnings;
 
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');  # All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
 
 
sub default_options {
    my ($self) = @_;
    return {
        %{ $self->SUPER::default_options() },               # inherit other stuff from the base class
 
        'pipeline_name' => 'split_fasta',                   # name used by the beekeeper to prefix job names on the farm
 
            # runnable-specific parameters' defaults:
        'max_chunk_length'  => 500000,
        'output_prefix'     => 'chunk_number_',
        'output_suffix'     => '.fasta',
 
        'chunks_dir'        => 'fasta_split_chunks',
    };
}
 
 
sub pipeline_create_commands {
    my ($self) = @_;
    return [
        @{$self->SUPER::pipeline_create_commands},  # inheriting database and hive tables' creation
 
        'mkdir -p '.$self->o('chunks_dir'),
    ];
}
 
 
sub pipeline_analyses {
    my ($self) = @_;
    return [
        {   -logic_name => 'split_fasta',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::FastaFactory',
            -input_ids => [ {
                'inputfile'         => $self->o('inputfile'),
                'max_chunk_length'  => $self->o('max_chunk_length'),
                'output_prefix'     => $self->o('chunks_dir').'/'.$self->o('output_prefix'),
                'output_suffix'     => $self->o('output_suffix'),
            } ],
            -flow_into => {
                2 => [ 'align' ],   # will create a fan of jobs
            },
        },
 
        {   -logic_name    => 'align',
            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
        },
    ];
}
 
1;