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wants to merge 345 commits into from
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Pseudo PR against TEMPLATE for checking the pipeline #33

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JudithBernett
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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/drugresponseeval 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>).
  • 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).

JudithBernett and others added 30 commits October 4, 2024 16:33
@JudithBernett
consolidating results! Now works for --models SingleDrugRandomForest …
f95a292 
…--baselines NaivePredictor with randomization and robustness test.
@JudithBernett
pipeline also works for cross validation now
417bac2
@JudithBernett
fixed that hyperparameter split is just executed per model class, not…
09d7b71 
… model instance
@JudithBernett
fixed error in consolidate_results.py
b4d8185
@JudithBernett
had limited cpus to 3
6f3d58a
@JudithBernett
trying to have gpu support
71467ba
@JudithBernett
trying to have gpu support pt. 2: only for specific models
8669fd3
@JudithBernett
doesn't work yet - setting label to process_gpu everywhere for now
bb5480b
@JudithBernett
doesn't work yet - setting label to process_gpu everywhere for now
7a6f4f0
@JudithBernett
forgot the brackets
bad410f
@JudithBernett
copying results
2fa47e7
@JudithBernett
more cpus for train_and_predict
0ca4213
@JudithBernett
incorporated updates from the package
a09503b
@JudithBernett
Merge branch 'dev' into nf-core-template-merge-3.0.1
c8c3a1a
@JudithBernett
fixed pre-commit
27d583d
@JudithBernett
Merge branch 'nf-core-template-merge-3.0.1' into single_model_restruc…
3ad2c3d 
…turing
@JudithBernett
Merge pull request #10 from nf-core/nf-core-template-merge-3.0.1
d3a8864 
Important! Template update for nf-core/tools v3.0.1
@JudithBernett
Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev
f565bd5
@JudithBernett
removed fastqc, multiqc. Removed max_multiqc_email_size from schema. …
f0742f6 
…Added input=null for linting in the nextflow.config
@JudithBernett
changed gitignore to include intellij .idea folder
246d54d
@JudithBernett
fixed linting
eed2178
@JudithBernett
fixed pre-commit
7e02d44
@JudithBernett
trying to get the new logos
a6acf53
@JudithBernett
new logos
39826d5
@JudithBernett
new logos
30d4990
@JudithBernett
going to document more
1ed774a
@JudithBernett
trying to fix the images
29cd07d
@JudithBernett
trying to fix images #2
a8622e7
@JudithBernett
trying to fix logo part 3
e10534d
@JudithBernett
Found the problem. The hack is to switch to the TEMPLATE branch and c…
a3fa5c4 
…opy the logo files from there and move them over.
JudithBernett and others added 29 commits June 20, 2025 14:07
@JudithBernett
added output and usage information
5e46315
@JudithBernett
this does not need resources
e83aeda
@JudithBernett
forgot response transformation on training final model
782798e
@JudithBernett
drevalpy v 1.3.4
430b13c
@JudithBernett
removed PR TEMPLATE changes
668a60c
@JudithBernett
Merge pull request #43 from nf-core/update_1_3_3
00ebfdd 
Update to drevalpy v1.3.4
@JudithBernett
Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev
a67cf54
@JudithBernett
new visualization function, minor fixes (don't need the no_refitting …
ff50958 
…parameter in load response because of the preprocess workflow, split early stopping no longer private method, cast path to str)
@JudithBernett
new version out
d95f920
@JudithBernett
updated changelog
0b791e3
@JudithBernett
updated snap
7822c98
@JudithBernett
I was wrong about needing local envs for nf-test, turns out all I nee…
5aa7976 
…ded was double quotes
@JudithBernett
I was wrong about needing local envs for nf-test, turns out all I nee…
0196926 
…ded was double quotes. Also added dates to changelog and https to the CITATIONS.md
@JudithBernett
Merge pull request #44 from nf-core/update_1_3_5
42dd2a3 
Update Drevalpy v1.3.5
@JudithBernett
default singularity container, hopefully it's smaller?
3b8b666
@JudithBernett
Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev
18fb55f
@JudithBernett
temporarily also running singularity test
67b2f8d
@JudithBernett
as singularity works now, reverting the test change. Also fixing the …
ea43180 
…precommit
@JudithBernett
updated changelog
de7da6e
@JudithBernett
Merge pull request #45 from nf-core/singularity
20ae699 
Custom Singularity container
@JudithBernett
updated changelog. Also gave the version a name
5ccd27f
@JudithBernett
Merge branch 'dev' into update_changelog
21b4841
@JudithBernett
Merge pull request #46 from nf-core/update_changelog
e76d25c 
Update changelog
@JudithBernett
Merge branch 'dev' into singularity
94ad418
@JudithBernett
Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev
955a950
@JudithBernett
Merge branch 'dev' into singularity
8917841
@JudithBernett
revert to docker, change to large runner, temporarily run singularity…
b01558c 
… to test
@JudithBernett
updated changelog, changed nf-test.yml back so that singularity is on…
276ef3b 
…ly run for PRs on main
@JudithBernett
Merge pull request #53 from nf-core/singularity
8fd6f24 
Revert to docker image, change to large runner
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5 participants
@JudithBernett @nf-core-bot @picciama @PascalIversen @mashehu