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nf-core/eager: [2.3.5] - Aalen (Patch) - 2021-06-04

James A. Fellows Yates; Alexander Peltzer; Thiseas C. Lamnidis; Maxime Borry; ZandraFagernas; Ido Bar; Aida Andrades Valtueña; alexandregilardet; nf-core bot; Maxime U. Garcia; Evan Floden; Phil Ewels; Patrick Hüther; Charles Plessy; Gisela Gabernet; sc13-bioinf; Åshild J. Vågene; Harshil Patel; Olga Botvinnik; Selina Carlhoff; Alex Hübner


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  <identifier identifierType="DOI">10.5281/zenodo.4898765</identifier>
  <creators>
    <creator>
      <creatorName>James A. Fellows Yates</creatorName>
      <affiliation>LMU München</affiliation>
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    <creator>
      <creatorName>Alexander Peltzer</creatorName>
      <affiliation>Boehringer Ingelheim</affiliation>
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    <creator>
      <creatorName>Thiseas C. Lamnidis</creatorName>
      <affiliation>Max Planck Institute for the Science of Human History</affiliation>
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      <creatorName>Maxime Borry</creatorName>
      <affiliation>Max Planck institute for the Science of Human Evolution</affiliation>
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      <affiliation>Griffith University</affiliation>
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    <creator>
      <creatorName>Aida Andrades Valtueña</creatorName>
      <affiliation>Max Planck Institute for the Science of Human History</affiliation>
    </creator>
    <creator>
      <creatorName>alexandregilardet</creatorName>
      <affiliation>The Francis Crick Institute</affiliation>
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      <creatorName>nf-core bot</creatorName>
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    <creator>
      <creatorName>Maxime U. Garcia</creatorName>
      <affiliation>@SciLifeLab | Karolinska Institutet</affiliation>
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    <creator>
      <creatorName>Evan Floden</creatorName>
      <affiliation>Seqera Labs and @nextflow-io</affiliation>
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    <creator>
      <creatorName>Phil Ewels</creatorName>
      <affiliation>Science for Life Laboratory</affiliation>
    </creator>
    <creator>
      <creatorName>Patrick Hüther</creatorName>
    </creator>
    <creator>
      <creatorName>Charles Plessy</creatorName>
    </creator>
    <creator>
      <creatorName>Gisela Gabernet</creatorName>
      <affiliation>@qbicsoftware</affiliation>
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      <creatorName>Åshild J. Vågene</creatorName>
    </creator>
    <creator>
      <creatorName>Harshil Patel</creatorName>
      <affiliation>The Francis Crick Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Olga Botvinnik</creatorName>
      <affiliation>@czbiohub</affiliation>
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    <creator>
      <creatorName>Selina Carlhoff</creatorName>
      <affiliation>MPI-SHH</affiliation>
    </creator>
    <creator>
      <creatorName>Alex Hübner</creatorName>
    </creator>
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  <titles>
    <title>nf-core/eager: [2.3.5] - Aalen (Patch) - 2021-06-04</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <dates>
    <date dateType="Issued">2021-06-04</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
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    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/nf-core/eager/tree/2.3.5</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1465061</relatedIdentifier>
  </relatedIdentifiers>
  <version>2.3.5</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;code&gt;Added&lt;/code&gt;
&lt;ul&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/722"&gt;#722&lt;/a&gt; - Adds bwa &lt;code&gt;-o&lt;/code&gt; flag for more flexibility in bwa parameters&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/736"&gt;#736&lt;/a&gt; - Add printing of multiqc run report location on successful completion&lt;/li&gt;
&lt;li&gt;New logo that is more visible when a user is using darkmode on GitHub or nf-core website!&lt;/li&gt;
&lt;/ul&gt;
&lt;code&gt;Fixed&lt;/code&gt;
&lt;ul&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/723"&gt;#723&lt;/a&gt; - Fixes empty fields in TSV resulting in uninformative error&lt;/li&gt;
&lt;li&gt;Updated template to nf-core/tools 1.14&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/688"&gt;#688&lt;/a&gt; - Clarified the pipeline is not just for humans and microbes, but also plants and animals, and also for modern DNA&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/751"&gt;#751&lt;/a&gt; - Added missing label to mtnucratio&lt;/li&gt;
&lt;li&gt;General code cleanup and standardisation of parameters with no default setting&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/750"&gt;#750&lt;/a&gt; - Fixed piped commands requesting the same number of CPUs at each command step&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/757"&gt;#757&lt;/a&gt; - Removed confusing 'Data Type' variable from MultiQC workflow summary (not consistent with TSV input)&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/759"&gt;#759&lt;/a&gt; - Fixed malformed software scraping regex that resulted in N/A in MultiQC report&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/759"&gt;#761&lt;/a&gt; - Fixed issues related to instability of samtools filtering related CI tests&lt;/li&gt;
&lt;/ul&gt;
&lt;code&gt;Dependencies&lt;/code&gt;
&lt;code&gt;Deprecated&lt;/code&gt;</description>
  </descriptions>
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