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Add ion annotation feature #229

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merged 4 commits into from Nov 14, 2022
Merged

Add ion annotation feature #229

merged 4 commits into from Nov 14, 2022

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jonasscheid
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@jonasscheid jonasscheid commented Nov 14, 2022 •
edited

This implements the feature requested in #220. A new folder created under intermediate_results/ion_annotations, where 2 files for each sample can be found:

  • _all_ions.tsv
  • _matching_ions.tsv

where _all_ions.tsv looks like this:

Ion_ID Peptide Experimental_mass Intensity Is_matching_ion nativeID filename
0 VVLYPLVAK 70.06599260489247 27419.54 True controllerType=0 controllerNumber=1 scan=48318 MM15_Melanom_1_A_1.mzML

and the _matching_ions.tsv as follows:

Peptide Ion_name Ion_charge Theoretical_mass Experimental_mass Intensity Ion_ID
VVLYPLVAK y1+ 1 70.0656 70.06599260489247 27419.5390625 0

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/mhcquant branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
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  • 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 Nov 14, 2022 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0c2f3dd

+| ✅ 156 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-14 13:26:44

marissaDubbelaar
marissaDubbelaar reviewed Nov 14, 2022
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@jonasscheid jonasscheid merged commit 6350048 into nf-core:dev Nov 14, 2022
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

This was referenced Nov 14, 2022
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@marissaDubbelaar marissaDubbelaar mentioned this pull request Nov 17, 2022
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