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Install Ascat with bioconda #32

Merged
merged 4 commits into from
Sep 5, 2019
Merged

Install Ascat with bioconda #32

merged 4 commits into from
Sep 5, 2019

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maxulysse
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  • Install ASCAT 2.5.2 with conda in the environment.yml file
  • Changed r-base from 3.5.1 to 3.4.1 and bioconductor-rtracklayer from 1.42.1 to 1.38.3 to satisfy conda dependencies when adding ASCAT to the recipe

@malinlarsson is working on updating ASCAT, so I'm adding it to the base docker container so we can have a clean conda install with all tools.

Many thanks to contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

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/sarek 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

Learn more about contributing: https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md

@maxulysse maxulysse self-assigned this Sep 5, 2019
@maxulysse maxulysse requested a review from a team September 5, 2019 07:51
@maxulysse maxulysse merged commit 747f8cd into nf-core:dev Sep 5, 2019
@maxulysse maxulysse deleted the ascat branch September 5, 2019 12:08
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2 participants