<commit_before>use VRPipe::Base;

class VRPipe::Pipelines::bam_genotype_checking with VRPipe::PipelineRole {
    method name {
        return 'bam_genotype_checking';
    }
    method _num_steps {
        return 4;
    }
    method description {
        return 'Check that the genotype of bam files matches the genotype of the samples they claim to be of.';
    }
    method steps {
        $self->throw("steps cannot be called on this non-persistent object");
    }
    
    method _step_list {
        return ([ VRPipe::Step->get(name => 'bin2hapmap_sites'),#1
                  VRPipe::Step->get(name => 'mpileup_bcf_hapmap'),#2
                  VRPipe::Step->get(name => 'glf_check_genotype'),#3
                  VRPipe::Step->get(name => 'gtypex_genotype_analysis'),#4
                  ],
                 
                 [ VRPipe::StepAdaptorDefiner->new(from_step => 0, to_step => 1, to_key => 'hapmap_file'),
                   VRPipe::StepAdaptorDefiner->new(from_step => 0, to_step => 2, to_key => 'bam_files'),
                   VRPipe::StepAdaptorDefiner->new(from_step => 1, to_step => 2, from_key => 'hapmap_file', to_key => 'hapmap_file'),
                   VRPipe::StepAdaptorDefiner->new(from_step => 2, to_step => 3, from_key => 'bcf_files_with_metadata', to_key => 'bcf_files'),
                   VRPipe::StepAdaptorDefiner->new(from_step => 3, to_step => 4, from_key => 'gtypex_files_with_metadata', to_key => 'gtypex_files'),
                   ],
                 
                 [ VRPipe::StepBehaviourDefiner->new(after_step => 4, behaviour => 'delete_outputs', act_on_steps => [1,2], regulated_by => 'cleanup', default_regulation => 0),]);
    }
}

1;<commit_msg>removed extraneous step adaptor, which prevented pipeline-setup from working with this pipeline<commit_after>use VRPipe::Base;

class VRPipe::Pipelines::bam_genotype_checking with VRPipe::PipelineRole {
    method name {
        return 'bam_genotype_checking';
    }
    method _num_steps {
        return 4;
    }
    method description {
        return 'Check that the genotype of bam files matches the genotype of the samples they claim to be of.';
    }
    method steps {
        $self->throw("steps cannot be called on this non-persistent object");
    }
    
    method _step_list {
        return ([ VRPipe::Step->get(name => 'bin2hapmap_sites'),#1
                  VRPipe::Step->get(name => 'mpileup_bcf_hapmap'),#2
                  VRPipe::Step->get(name => 'glf_check_genotype'),#3
                  VRPipe::Step->get(name => 'gtypex_genotype_analysis'),#4
                  ],
                 
                 [ VRPipe::StepAdaptorDefiner->new(from_step => 0, to_step => 2, to_key => 'bam_files'),
                   VRPipe::StepAdaptorDefiner->new(from_step => 1, to_step => 2, from_key => 'hapmap_file', to_key => 'hapmap_file'),
                   VRPipe::StepAdaptorDefiner->new(from_step => 2, to_step => 3, from_key => 'bcf_files_with_metadata', to_key => 'bcf_files'),
                   VRPipe::StepAdaptorDefiner->new(from_step => 3, to_step => 4, from_key => 'gtypex_files_with_metadata', to_key => 'gtypex_files'),
                   ],
                 
                 [ VRPipe::StepBehaviourDefiner->new(after_step => 4, behaviour => 'delete_outputs', act_on_steps => [1,2], regulated_by => 'cleanup', default_regulation => 0),]);
    }
}

1;
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