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Bug fixes and module updates #874

Merged
merged 9 commits into from
Sep 29, 2022
Merged

Bug fixes and module updates #874

merged 9 commits into from
Sep 29, 2022
+284 −80

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drpatelh
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@drpatelh drpatelh commented Sep 27, 2022 •
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Fixes

  • [#746] - Add tin.py output to MultiQC report
  • [#841] - Turn --deseq2_vst on by default
  • [#857] - Missing parameter required by StringTie if using STAR as aligner
  • [#862] - Filter samples that have no reads after trimming

Update all nf-core/modules

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github-actions bot commented Sep 27, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 660cac3

+| ✅ 151 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.5.1
  • Run at 2022-09-28 15:49:05

@drpatelh
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Github actions is failing because it can't find the version of NF to download and isn't related to the pipeline itself...weird...

Error: Could not retrieve Nextflow release matching 21.10.3.

@robsyme
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robsyme commented Sep 28, 2022 •
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Does the workflow need to be so strict in defining the Nextflow version?

The ! prefix in manifest.nextflowVersion forces exactly 21.10.3, which is more than a year old now.

I don't want to distract too much from the real changes in the PR, but the error above made me realise that rnaseq is being quite strict.

@jfy133
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jfy133 commented Sep 29, 2022

we are getting the same errors on funcscan:

https://github.com/nf-core/funcscan/actions/runs/3149654684/jobs/5121557320

The error is coming from here (but I know 0 abot typescript...)

https://github.com/nf-core/setup-nextflow/blob/701d0b9769983d180721056d76d35de927800b27/index.ts#L120-L132

MatthiasZepper
MatthiasZepper approved these changes Sep 29, 2022
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@MatthiasZepper MatthiasZepper left a comment •
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Very nice work and looking forward to release 3.9!

(I haven't reviewed the updated modules, but I suppose that they have already been vetted before being updated in the modules repo.)

Sadly, umi-tools has not seen any recent update despite the important bug fix, so I think there is no point in delaying a new pipeline release for that improvement.

@drpatelh
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The ! prefix in manifest.nextflowVersion forces exactly 21.10.3, which is more than a year old now.

Actually, this appears to make it the minimum release rather than the required release. Running with 21.10.2 should break the pipeline which is what we want, however, running with a more recent release will be tolerated. I suspect the Nextflow docs may be wrong about this.

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drpatelh commented Sep 29, 2022 •
edited by jfy133
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we are getting the same errors on funcscan:

This appears to be an issue specific to Github Actions because I can pull the assets for that release locally😬

Yup, agreed! Same for me!

@drpatelh drpatelh merged commit 12c65eb into nf-core:dev Sep 29, 2022
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@drpatelh @robsyme @jfy133 @MatthiasZepper