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Moving error-handling to script section of sentieon-processes #1164

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Moving error-handling to script section of sentieon-processes #1164

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asp8200
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@asp8200 asp8200 commented Jul 26, 2023 •
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DON'T MERGE! This PR is only for testing the "fix" 😊

The problem If one tries to run this test

nextflow run main.nf -profile test_cache,conda --outdir results

on the dev-branch, then one gets the following error msg:

ERROR ~ Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead.

See also https://nfcore.slack.com/archives/C02MDBZAYJK/p1690379840650269

With this PR, the above-mentioned test can now be executed locally. Moreover, when one tries to run the same test with sentieon-bwamem, that is,

nextflow run main.nf -profile test_cache,conda --aligner sentieon-bwamem --outdir results

one get's

ERROR ~ Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead.

That is as it should be.

If all else ok, then I'll make the same change to the sentieon-modules over in the nf-core/modules-repo, and then make a proper PR for Sarek.

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/sarek 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 --outdir <OUTDIR>).
  • 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 26, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 2bd82d7

+| ✅ 152 tests passed       |+
#| ❔   9 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-26 14:48:14

@asp8200
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asp8200 commented Aug 3, 2023

This problem was now solved in the modules-repo ( nf-core/modules#3683 ) , and I'll update the sentieon-modules in Sarek accordingly in a fresh PR.

@asp8200 asp8200 closed this Aug 3, 2023
@maxulysse maxulysse deleted the sentieon_err_handling branch September 18, 2023 16:26
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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen will be requested when the pull request is marked ready for review FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse will be requested when the pull request is marked ready for review maxulysse is a code owner

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