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Add a new sample field to meta #425

Merged
merged 6 commits into from
Sep 15, 2023
Merged

Add a new sample field to meta #425

merged 6 commits into from
Sep 15, 2023

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ramprasadn
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@ramprasadn ramprasadn commented Sep 13, 2023 •
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PR checklist

We used to add "_T[linenumber]" to sample id to differentiate between data from different lanes. Then before merging bam files from multiple lanes into one file, we split based on "_T" to get the sample id back. This could potentially cause issues when the sample name has an _T. To avoid that, I have created a new field sample in the meta which also contains the user given sample id. Before the merging step the value from the sample field will be copied into id.

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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 Sep 13, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0a4fb90

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-15 12:40:33

@ramprasadn ramprasadn marked this pull request as ready for review September 13, 2023 15:23
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asp8200 commented Sep 14, 2023

Damn! "no space left on device."!

Command error:
  Unable to find image 'quay.io/biocontainers/hmtnote:0.7.2--pyhdfd78af_1' locally
  0.7.2--pyhdfd78af_1: Pulling from biocontainers/hmtnote
  c1a16a04cedd: Already exists
  4ca545ee6d5d: Already exists
  8c4452938393: Pulling fs layer
  8c4452938393: Verifying Checksum
  8c4452938393: Download complete
  docker: failed to register layer: mkdir /usr/local/lib/python3.10/site-packages/pomegranate-0.14.8.dist-info: no space left on device.

@ramprasadn
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Yeah, I guess I have to start thinking about turning off some of the process for the github ci, so that we can avoid this error 😅

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ramprasadn commented Sep 15, 2023 •
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mt_analysis uses a few large containers so I have turned it off to save space in the runner. But I haven't turned it off for the test_one_sample profile so at least we are testing that workflow partially.

Hopefully, we can switch to nf-test soon, and all these issues will go away 😅

jemten
jemten approved these changes Sep 15, 2023
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Looks good to me! Nice to not rely on string splitting to get the sample id.

@ramprasadn ramprasadn merged commit 0ad16db into nf-core:dev Sep 15, 2023
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@jemten jemten mentioned this pull request Sep 27, 2023
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@ramprasadn ramprasadn deleted the addsampletometa branch February 2, 2024 16:57
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@jemten jemten jemten approved these changes

@asp8200 asp8200 Awaiting requested review from asp8200

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@ramprasadn @asp8200 @jemten