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Add Readgroups to Salmon Branch #240

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Add Readgroups to Salmon Branch #240

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apeltzer
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Adding the sequencing center was done a while ago to have properly set ReadGroups in the BAM files created by HiSAT2 or STAR. However, this isn't enough when using any tool or library based on the picard/GATK htsjdk, that checks for certain required readgroup information to be present in BAM files and corresponding headers (not only when sequencing center is set, but in all cases!). This caused QualiMap to fail unfortunately, which @olgabot found out here: #238

This PR adds the SM information to both HISAT2 and STAR and adds in the defaults without sequencing centers to be added in all cases, otherwise QualiMap will also fail when seqCenter isn't set by the user!

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Happy to add more RG information, if this is necessary (we should maybe test/check this out @olgabot ?)

@apeltzer
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I'll branch from the current Salmon branch now and will create a new PR then.

@apeltzer apeltzer closed this Jun 23, 2019
@apeltzer apeltzer deleted the add-readgroups branch June 23, 2019 12:03
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2 participants