Software Open Access

Janis: A Python framework for Portable Pipelines

Lupat, Richard; Franklin, Michael; Thomas, Evan; Kesumadewi, Juny; Yu, Jiaan; Bhuyan, Mohammad; Papenfuss, Tony; Park, Daniel; Pope, Bernard; Li, Jason


DataCite XML Export

<?xml version='1.0' encoding='utf-8'?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd">
  <identifier identifierType="DOI">10.5281/zenodo.4427231</identifier>
  <creators>
    <creator>
      <creatorName>Lupat, Richard</creatorName>
      <givenName>Richard</givenName>
      <familyName>Lupat</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-6435-7100</nameIdentifier>
      <affiliation>Peter MacCallum Cancer Centre</affiliation>
    </creator>
    <creator>
      <creatorName>Franklin, Michael</creatorName>
      <givenName>Michael</givenName>
      <familyName>Franklin</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-9292-1533</nameIdentifier>
      <affiliation>University of Melbourne, Peter MacCallum Cancer Centre</affiliation>
    </creator>
    <creator>
      <creatorName>Thomas, Evan</creatorName>
      <givenName>Evan</givenName>
      <familyName>Thomas</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7742-2031</nameIdentifier>
      <affiliation>Walter and Eliza Hall Institute of Medical Research</affiliation>
    </creator>
    <creator>
      <creatorName>Kesumadewi, Juny</creatorName>
      <givenName>Juny</givenName>
      <familyName>Kesumadewi</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1931-8521</nameIdentifier>
      <affiliation>University of Melbourne</affiliation>
    </creator>
    <creator>
      <creatorName>Yu, Jiaan</creatorName>
      <givenName>Jiaan</givenName>
      <familyName>Yu</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2366-1165</nameIdentifier>
      <affiliation>Peter MacCallum Cancer Centre</affiliation>
    </creator>
    <creator>
      <creatorName>Bhuyan, Mohammad</creatorName>
      <givenName>Mohammad</givenName>
      <familyName>Bhuyan</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-9292-1533</nameIdentifier>
      <affiliation>Walter and Eliza Hall Institute of Medical Research</affiliation>
    </creator>
    <creator>
      <creatorName>Papenfuss, Tony</creatorName>
      <givenName>Tony</givenName>
      <familyName>Papenfuss</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1102-8506</nameIdentifier>
      <affiliation>Walter and Eliza Hall Institute of Medical Research</affiliation>
    </creator>
    <creator>
      <creatorName>Park, Daniel</creatorName>
      <givenName>Daniel</givenName>
      <familyName>Park</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-6354-0931</nameIdentifier>
      <affiliation>University of Melbourne</affiliation>
    </creator>
    <creator>
      <creatorName>Pope, Bernard</creatorName>
      <givenName>Bernard</givenName>
      <familyName>Pope</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-4840-1095</nameIdentifier>
      <affiliation>University of Melbourne</affiliation>
    </creator>
    <creator>
      <creatorName>Li, Jason</creatorName>
      <givenName>Jason</givenName>
      <familyName>Li</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1150-3549</nameIdentifier>
      <affiliation>Peter MacCallum Cancer Centre</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Janis: A Python framework for Portable Pipelines</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>janis</subject>
    <subject>pipelines</subject>
    <subject>containers</subject>
    <subject>commonwl</subject>
    <subject>wdl</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-01-08</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4427231</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4427230</relatedIdentifier>
  </relatedIdentifiers>
  <version>v0.11.0</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;ul&gt;
	&lt;li&gt;GitHub: &lt;a href="https://github.com/PMCC-BioinformaticsCore/janis"&gt;https://github.com/PMCC-BioinformaticsCore/janis&lt;/a&gt;
	&lt;ul&gt;
		&lt;li&gt;v0.11.0:&amp;nbsp;&lt;a href="https://github.com/PMCC-BioinformaticsCore/janis/releases/tag/v0.11.0"&gt;https://github.com/PMCC-BioinformaticsCore/janis/releases/tag/v0.11.0&lt;/a&gt;&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;Documentation:&amp;nbsp;&lt;a href="https://janis.readthedocs.io/en/latest/"&gt;https://janis.readthedocs.io/en/latest/&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;There are many frameworks for building bioinformatics pipelines, including the Common Workflow Language (CWL), Workflow Description Language (WDL), Nextflow and more. Each framework brings a community and a set of resources, including engines and other tools. The incompatibility of these frameworks poses considerable challenges for portability, where changing between systems requires substantial re-engineering efforts and is an inhibitor to sharing workflows. There are many external differences in these frameworks, such as implementation language, however they have a considerable overlap in their underlying features.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;Janis is an open-source Python framework that addresses this interoperability problem by abstracting the workflow model in order to generate CWL and WDL pipelines. The Janis API simplifies many aspects of building workflows and can mask idiosyncrasies of the target specifications while still allowing for rich workflow logic to be represented.&lt;/p&gt;

&lt;p&gt;Janis includes two exemplar variant calling pipelines for calling germline and somatic variants.&lt;/p&gt;</description>
  </descriptions>
</resource>
98
4
views
downloads
All versions This version
Views 9898
Downloads 44
Data volume 38.6 MB38.6 MB
Unique views 8787
Unique downloads 44

Share

Cite as