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Added kallistobustools #56

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merged 10 commits into from Apr 27, 2021
Merged

Added kallistobustools #56

merged 10 commits into from Apr 27, 2021

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KevinMenden
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This PR adds a first, working version of the kb or kallistobustools pipeline.

These steps are currently implemented:

  • input check
  • gene map creation (if not given)
  • kb ref (if index not given)
  • kb count
  • get software versions
  • multiqc

The MultiQC output is a bit sad though, as there doesn't exist a module for kb.

@KevinMenden
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Further additions:

  • added groovy function to adjust the protocol parameter, removed the chemistry parameter
  • got the tests working
  • updated schema and the NfcoreSchema class

The lint test is failing because the NfcoreSchema.groovy file is from the dev branch of nf-core tools.

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@ggabernet ggabernet left a comment

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Looking great, I only had a couple of comments, and anyways the "valid" review will be the one to dev or master

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@@ -56,6 +49,17 @@
"default": "alevin",
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This param should probably also be an enumeration enum, so that it can validate that the options are valid, right?

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Absolutely, still need to have another look over the Schema :)

@KevinMenden
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Thanks a lot for the review @ggabernet ! :)

KevinMenden and others added 2 commits April 27, 2021 09:34
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
@KevinMenden KevinMenden merged commit 52d902b into nf-core:dsl2 Apr 27, 2021
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2 participants