8000 Increment support of netmhc tools by jonasscheid · Pull Request #166 · nf-core/epitopeprediction · GitHub
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Increment support of netmhc tools #166

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Merged
merged 3 commits into from
Jul 6, 2022
Merged

Increment support of netmhc tools #166

merged 3 commits into from
Jul 6, 2022

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jonasscheid
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@jonasscheid jonasscheid commented Jul 5, 2022 •
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This PR increments the number of supported netmhc tools for class 1 and 2 for linux and Mac OS based systems:

  • NetMHCpan 4.1
  • NetMHCII 2.2 (Mac OS)
  • NetMHCII 2.3
  • NetMHCIIpan 4.0
  • NetMHCIIpan 4.1

For further documentation:
NetMHCIIpan 4.1 (Darwin & Linux) provid the data folder within the software tar, however we did not yet work around this problem. I just thought it would be of nice to have it in order to come up with a solution for this specific version. Meaning the data url and md5 will be deleted most likely.

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 you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/epitopeprediction branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 5, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 59139ad

+| ✅ 150 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-06 13:59:12

christopher-mohr
christopher-mohr reviewed Jul 6, 2022
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LGTM, just two comments

jonasscheid
jonasscheid commented Jul 6, 2022
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assets/external_tools_meta.json
"data_md5": "ec3032cb66aee20ff0f53ff7f1795f47",
"binary_name": "netMHCIIpan"
},
"4.1": {
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Also for documentation:
NetMHCIIpan 4.1 (Darwin & Linux) provid the data folder within the software tar, however we did not yet work around this problem. I just thought it would be of interest to have it in order to come up with a solution for this specific version

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Yes, we should definietly check if we can optimise the process for this case.

@christopher-mohr christopher-mohr merged commit 068eb71 into nf-core:switch_to_epytope Jul 6, 2022
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@christopher-mohr christopher-mohr christopher-mohr approved these changes

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