Kwalitee Issues

has_changelog

Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.

package_version_matches_dist_version

Fix the version(s).

use_strict

Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.

Error: Bio::VertRes::Config::Exceptions

has_meta_json

Add a META.json to the distribution. Your buildtool should be able to autogenerate it.

meta_yml_declares_perl_version

If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.

Error: Bio::VertRes::Config::Exceptions

meta_yml_has_provides

Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.

Modules

Name Abstract Version View
Bio::VertRes::Config Create config files for the vr-codebase pipelines metacpan
Bio::VertRes::Config::CommandLine::BacteriaAssemblyAndAnnotation Create assembly and annotation files metacpan
Bio::VertRes::Config::CommandLine::BacteriaAssemblySingleCell Create assembly and annotation files metacpan
Bio::VertRes::Config::CommandLine::BacteriaMapping Create config scripts to map bacteria metacpan
Bio::VertRes::Config::CommandLine::BacteriaRegisterAndQCStudy Create config scripts to map helminths metacpan
Bio::VertRes::Config::CommandLine::BacteriaRnaSeqExpression Create config scripts to map and run the rna seq expression pipeline metacpan
Bio::VertRes::Config::CommandLine::BacteriaSnpCalling Create config scripts to map and snp call bacteria. metacpan
Bio::VertRes::Config::CommandLine::Common Create config scripts metacpan
Bio::VertRes::Config::CommandLine::ConstructLimits Put the limits together metacpan
Bio::VertRes::Config::CommandLine::EukaryotesAssembly Create assembly files metacpan
Bio::VertRes::Config::CommandLine::EukaryotesMapping Create config scripts to map eukaryotes metacpan
Bio::VertRes::Config::CommandLine::EukaryotesRegisterAndQCStudy Create config scripts to map helminths metacpan
Bio::VertRes::Config::CommandLine::EukaryotesRnaSeqExpression Create config scripts to map and run the rna seq expression pipeline metacpan
Bio::VertRes::Config::CommandLine::EukaryotesSnpCalling Create config scripts to map and snp call bacteria. metacpan
Bio::VertRes::Config::CommandLine::HelminthMapping Create config scripts to map helminths metacpan
Bio::VertRes::Config::CommandLine::HelminthRegisterAndQCStudy Create config scripts to map helminths metacpan
Bio::VertRes::Config::CommandLine::HelminthRnaSeqExpression Create config scripts to map and run the rna seq expression pipeline metacpan
Bio::VertRes::Config::CommandLine::HelminthSnpCalling Create config scripts to map and snp call bacteria. metacpan
Bio::VertRes::Config::CommandLine::LogParameters A class to represent multiple top level files. It splits out mixed config files into the correct top level files metacpan
Bio::VertRes::Config::CommandLine::ReferenceHandlingRole A role to handle references in a command line script metacpan
Bio::VertRes::Config::CommandLine::StudyNameSearch Prevent a study name from being registered in two different databases metacpan
Bio::VertRes::Config::CommandLine::VirusAssemblyAndAnnotation Create assembly and annotation files metacpan
Bio::VertRes::Config::CommandLine::VirusMapping Create config scripts to map viruses metacpan
Bio::VertRes::Config::CommandLine::VirusRegisterAndQCStudy Create config scripts to map helminths metacpan
Bio::VertRes::Config::CommandLine::VirusRnaSeqExpression Create config scripts to map and run the rna seq expression pipeline metacpan
Bio::VertRes::Config::CommandLine::VirusSnpCalling Create config scripts to map and snp call bacteria. metacpan
Bio::VertRes::Config::Exceptions Exceptions for input data metacpan
Bio::VertRes::Config::MultipleTopLevelFiles A class to represent multiple top level files. It splits out mixed config files into the correct top level files metacpan
Bio::VertRes::Config::Pipelines::AnnotateAssembly A class for generating the AnnotateAssembly pipeline config file which annotates an assembly metacpan
Bio::VertRes::Config::Pipelines::Assembly A base class for generating the Assembly pipeline config file which archives data to nfs units metacpan
Bio::VertRes::Config::Pipelines::BamImprovement The base class for the bam improvement pipeline. metacpan
Bio::VertRes::Config::Pipelines::Bowtie2Mapping Base class for the BWA mapper metacpan
Bio::VertRes::Config::Pipelines::BwaMapping Base class for the BWA mapper metacpan
Bio::VertRes::Config::Pipelines::Common A set of attributes common to all pipeline config files metacpan
Bio::VertRes::Config::Pipelines::Import A class for generating the Import pipeline config file metacpan
Bio::VertRes::Config::Pipelines::Mapping The base class for the mapping pipeline. metacpan
Bio::VertRes::Config::Pipelines::QC A class for generating the QC pipeline config file. This is done on a per study basis ususally (and filtered by species). metacpan
Bio::VertRes::Config::Pipelines::RnaSeqExpression The base class for the RNA seq expression and TraDis pipeline. metacpan
Bio::VertRes::Config::Pipelines::Roles::FilenameWithReference Moose Role to set the logfile name and config filename to include the reference metacpan
Bio::VertRes::Config::Pipelines::Roles::MetaDataFilter Moose Role for dealing with limits meta data filters metacpan
Bio::VertRes::Config::Pipelines::Roles::MultiplePrefix Moose Role for where you want different prefixes to allow you to run the same pipeline multiple times on the same data metacpan
Bio::VertRes::Config::Pipelines::Roles::RootDatabaseLookup Moose Role for translating non standard database names to their area metacpan
Bio::VertRes::Config::Pipelines::SmaltMapping Base class for the smalt mapper metacpan
Bio::VertRes::Config::Pipelines::SnpCalling The base class for the SNP calling pipeline. metacpan
Bio::VertRes::Config::Pipelines::SpadesAssembly A base class for generating an Assembly pipeline config file using spades metacpan
Bio::VertRes::Config::Pipelines::Ssaha2Mapping Base class for the Ssaha2 mapper metacpan
Bio::VertRes::Config::Pipelines::StampyMapping Base class for the Stampy mapper metacpan
Bio::VertRes::Config::Pipelines::Store A class for generating the Store pipeline config file which archives data to nfs units metacpan
Bio::VertRes::Config::Pipelines::TophatMapping Base class for the Tophat mapper metacpan
Bio::VertRes::Config::Pipelines::Tradis Create TraDIS config files metacpan
Bio::VertRes::Config::Pipelines::VelvetAssembly A base class for generating an Assembly pipeline config file using velvet metacpan
Bio::VertRes::Config::Recipes::BacteriaAssemblyAndAnnotation Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first metacpan
Bio::VertRes::Config::Recipes::BacteriaAssemblySingleCell Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first metacpan
Bio::VertRes::Config::Recipes::BacteriaMappingUsingBowtie2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaMappingUsingBwa Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaMappingUsingSmalt Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaMappingUsingSsaha2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaMappingUsingStampy Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaMappingUsingTophat Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaRegisterAndQCStudy Register and QC a study metacpan
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingBowtie2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingBwa Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingSmalt Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingStampy Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaRnaSeqExpressionUsingTophat Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingBowtie2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingBwa Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingSmalt Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingSsaha2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingStampy Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::Common Common base for recipes metacpan
Bio::VertRes::Config::Recipes::EukaryotesAssembly Create the assemblyfiles only, so no reference required, but for it to run you need to have done QC first metacpan
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingBowtie2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingBwa Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingSmalt Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingSsaha2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingStampy Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesMappingUsingTophat Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesRegisterAndQCStudy Register and QC a study metacpan
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingBowtie2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingBwa Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingSmalt Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingStampy Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesRnaSeqExpressionUsingTophat Standard snp calling pipeline for eukaryotes metacpan
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingBowtie2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingBwa Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingSmalt Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingSsaha2 Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingStampy Standard snp calling pipeline for bacteria metacpan
Bio::VertRes::Config::Recipes::Global Setting up global config files metacpan
Bio::VertRes::Config::Recipes::HelminthRegisterAndQCStudy Register and QC a study metacpan
Bio::VertRes::Config::Recipes::Roles::BacteriaMapping Moose Role which creates the Euk mapping objects metacpan
Bio::VertRes::Config::Recipes::Roles::BacteriaRegisterStudy Moose Role for registering a study metacpan
Bio::VertRes::Config::Recipes::Roles::BacteriaRnaSeqExpression Moose Role which creates the rna seq expression object metacpan
Bio::VertRes::Config::Recipes::Roles::BacteriaSnpCalling Moose Role which creates the bacteria snp calling object metacpan
Bio::VertRes::Config::Recipes::Roles::CreateGlobal Moose Role for creating all the global config files after creation metacpan
Bio::VertRes::Config::Recipes::Roles::EukaryotesMapping Moose Role which creates the Euk mapping objects metacpan
Bio::VertRes::Config::Recipes::Roles::EukaryotesRegisterStudy Moose Role for registering a study metacpan
Bio::VertRes::Config::Recipes::Roles::EukaryotesRnaSeqExpression Moose Role which creates the rna seq expression object metacpan
Bio::VertRes::Config::Recipes::Roles::EukaryotesSnpCalling Moose Role which creates the bacteria snp calling object metacpan
Bio::VertRes::Config::Recipes::Roles::Reference Attributes for working with references metacpan
Bio::VertRes::Config::Recipes::Roles::RegisterStudy Moose Role for registering a study metacpan
Bio::VertRes::Config::Recipes::Roles::VirusMapping Moose Role which creates the Euk mapping objects metacpan
Bio::VertRes::Config::Recipes::Roles::VirusRegisterStudy Moose Role for registering a study metacpan
Bio::VertRes::Config::Recipes::Roles::VirusRnaSeqExpression Moose Role which creates the rna seq expression object metacpan
Bio::VertRes::Config::Recipes::Roles::VirusSnpCalling Moose Role which creates the virus snp calling object metacpan
Bio::VertRes::Config::Recipes::VirusAssemblyAndAnnotation Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first metacpan
Bio::VertRes::Config::Recipes::VirusMappingUsingBowtie2 Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusMappingUsingBwa Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusMappingUsingSmalt Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusMappingUsingSsaha2 Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusMappingUsingStampy Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusMappingUsingTophat Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusRegisterAndQCStudy Register and QC a study metacpan
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingBowtie2 Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingBwa Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingSmalt Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingStampy Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusRnaSeqExpressionUsingTophat Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingBowtie2 Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingBwa Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingSmalt Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingSsaha2 Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::Recipes::VirusSnpCallingUsingStampy Standard snp calling pipeline for virus metacpan
Bio::VertRes::Config::References A class for translating between a reference name and the location on disk metacpan
Bio::VertRes::Config::RegisterStudy Register a study metacpan
Bio::VertRes::Config::TopLevel A top level config file for a pipeline metacpan
Bio::VertRes::Config::Types Moose types to use for validation. metacpan
Bio::VertRes::Config::Validate::File Check to see if a file exists. For validation when classes have input files. metacpan
Bio::VertRes::Config::Validate::Prefix Validates a prefix for use in filenames within the pipeline metacpan

Other Files

MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan
README.md metacpan
dist.ini metacpan