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Issue 162 add assembler qc report #167

Merged
merged 10 commits into from
Aug 28, 2023
Merged

Issue 162 add assembler qc report #167

merged 10 commits into from
Aug 28, 2023

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tfalkarkea
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • README.md is updated (including new tool citations and authors/contributors).

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Added a module for transrate, which is a simple way to create some quality control metrics for an assembly file. The CSV transrate generates is then included in the final MultiQC, which has some minor formatting adjustments included in assets/multiqc_config.yml.

Further changes may be useful to this MultiQC formatting.

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github-actions bot commented Aug 24, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6309064

+| ✅ 154 tests passed       |+
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.5.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-25 20:02:33

erikrikarddaniel
erikrikarddaniel reviewed Aug 24, 2023
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I think the module would be a good addition to the nf-core set of modules. A little more work, as you're required to provide tests, but usually worth it.

I have a question regarding whether the TRANSRATE module should unzip or not, see comment in the code. If the tool can be made to read gzipped files, that would be best, if not, let it take an unzipped file and feed it with the output from the UNPIGZ_CONTIGS module.

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tfalkarkea and others added 2 commits August 24, 2023 10:39
@tfalkarkea @erikrikarddaniel
Update workflows/metatdenovo.nf
5988655 
Adopting input change to transrate.

Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
@tfalkarkea
issue-162 created an unzipped contig channel, remove transrate gzip
d6b5878
erikrikarddaniel
erikrikarddaniel approved these changes Aug 25, 2023
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Looks fine. Just a tiny comment.

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danilodileo
danilodileo approved these changes Aug 28, 2023
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LGTM

@erikrikarddaniel erikrikarddaniel merged commit 59538cf into nf-core:dev Aug 28, 2023
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@erikrikarddaniel erikrikarddaniel mentioned this pull request Aug 28, 2023
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@tfalkarkea tfalkarkea deleted the issue-162-add-assembler-qc-report branch August 29, 2023 13:21
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@danilodileo danilodileo danilodileo approved these changes

@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@tfalkarkea @erikrikarddaniel @danilodileo