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feat: gene essentiality workflow #675

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feat: gene essentiality workflow #675

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07329bc
feat: gene essentiality workflow with pr comment
mihai-sysbio Jul 7, 2023
c3db9c5
Merge branch 'develop' into feat/gene-essentiality-workflow
mihai-sysbio Oct 6, 2023
1bba24d
chore: expand workflow targets
mihai-sysbio Oct 6, 2023
aff8211
fix: add to matlab path
mihai-sysbio Oct 6, 2023
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7 changes: 7 additions & 0 deletions .github/workflows/commentsFromTests.md
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This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the gene essentiality test:

<pre>
{TEST_RESULTS}
</pre>

> _Note: In the case of multiple test runs, this post will be edited._
32 changes: 32 additions & 0 deletions .github/workflows/gene-essentiality.yml
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name: Check gene essentiality with Hart 2015

on:
pull_request:
branches:
- "main"
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jobs:
check-metabolictasks:
runs-on: self-hosted

steps:
- name: Checkout
uses: actions/checkout@v3

- name: Run gene essentiality
id: essentiality
run: |
TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "ihuman = importYaml('Human-GEM.yml'); taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); eGenes = estimateEssentialGenes(ihuman, 'Hart2015_RNAseq.txt', taskStruct); disp(evaluateHart2015Essentiality(eGenes));" | awk 'NR>9 && !/^\.+/')
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@haowang-bioinfo the output of this line is very hard to capture/use. Do you have any suggestions to make this output more compact?

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As seen in this workflow run, the output is way too rich to fit in a PR comment. @haowang-bioinfo how would you suggest to change it to end up with a nice summary like here?

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no, I've never thought about this. Because they are non-binary indicators that are hard to be used for evaluating purpose in actions

PARSED_RESULTS="${TEST_RESULTS//'%'/'%25'}"
PARSED_RESULTS="${PARSED_RESULTS//$'\n'/'<br>'}"
PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'<br>'}"
echo "results=$PARSED_RESULTS" >> $GITHUB_OUTPUT

- name: Post comment
uses: NejcZdovc/comment-pr@v2
with:
file: "commentsFromTests.md"
env:
GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
TEST_RESULTS: ${{steps.essentiality.outputs.results}}
GH_ACTION_RUN: ${{github.run_id}}