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Fix mirtop quant conda env #350

Merged
merged 3 commits into from
May 7, 2024
Merged

Fix mirtop quant conda env #350

merged 3 commits into from
May 7, 2024

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christopher-mohr
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This fixes the conda env for the mirtop_quant process. The issue with pysam that is part of the env seems to be caused by the python version (3.6). Therefore, adding the python=3.7 dependency.

Related to #347.

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/smrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 May 7, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6a44ec2

+| ✅ 183 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-07 13:10:09

@maxulysse
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Can you update CHANGELOG too?

@christopher-mohr christopher-mohr merged commit 5ee9a64 into nf-core:dev May 7, 2024
10 checks passed
@christopher-mohr christopher-mohr deleted the fix_mirtop_conda branch May 7, 2024 13:36
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

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@christopher-mohr @maxulysse @nvnieuwk