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First release! #22

Merged
merged 122 commits into from
Jan 31, 2025
Merged

First release! #22

merged 122 commits into from
Jan 31, 2025

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JudithBernett
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@JudithBernett JudithBernett commented Jan 30, 2025 •
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Very excited to present the first release of the pipeline!
Details on how the pipeline works and should be used are in usage.md and output.md.

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 pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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
@nf-core-bot
Template update for nf-core/tools version 3.0.0
388888d
@nf-core-bot
Template update for nf-core/tools version 3.0.1
9a26032
@nf-core-bot
Template update for nf-core/tools version 3.0.2
825f400
@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
Merge branch 'TEMPLATE' of github.com:nf-core/drugresponseeval into T…
8a1d6ce 
…EMPLATE
@JudithBernett
going to document more
1ed774a
JudithBernett and others added 27 commits January 13, 2025 15:31
@JudithBernett
Merge branch 'nf-core-template-merge-3.1.1' into global_checkpoint_dir
a9f7167
@JudithBernett
Merge pull request #16 from nf-core/global_checkpoint_dir
da69223 
Global checkpoint dir
@JudithBernett
Merge branch 'dev' of https://github.com/picciama/drugresponseeval in…
f1f5e94 
…to dev
@JudithBernett
merged latest dev version
590f7c6
@JudithBernett
Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev
a33acb7
@JudithBernett
Merge branch 'dev' into fix/datapath
b0d8ac6
@JudithBernett
./data -> data
a8cd55f
@nf-core-bot
Template update for nf-core/tools version 3.1.2
8ac0bf0
@nf-core-bot
Template update for nf-core/tools version 3.2.0
b28687f
@JudithBernett
Lots of fixes:
65bfa0b 
- added params.measure
- made sure that downloaded data is exported to path_data but that internally, the work dir path is used (more nextflow-y)
- added the model_checkpoint_dirs everywhere
@JudithBernett
did not work with relative default path yet, maybe now
3797462
@JudithBernett
updated documentation
db805e9
@JudithBernett
Merge pull request #18 from nf-core/fix/datapath
3f276ec 
Fix/datapath
@JudithBernett
Merge branch 'dev' of https://github.com/picciama/drugresponseeval in…
eee9a57 
…to dev
@JudithBernett
merged latest dev version
f83dcde
@JudithBernett
Merge branch 'dev' into nf-core-template-merge-3.2.0
f24c762
@PascalIversen
Merge pull request #20 from nf-core/nf-core-template-merge-3.2.0
9f502d6 
Important! Template update for nf-core/tools v3.2.0
@JudithBernett
fixed schema
83b4f54
@JudithBernett
Merge branch 'dev' of https://github.com/picciama/drugresponseeval in…
b628a0d 
…to dev
@JudithBernett
Merge branch 'dev' into feature/curvecurator_module
35350da
@JudithBernett
fixed curvecurator-related tasks to work within the Nextflow logic, i…
a25e8d8 
….e., with the local paths in the work directories.

Updated output and usage documentation.
@JudithBernett
updated CITATIONS.md for curvecurator
c7452d8
@JudithBernett
updated CHANGELOG.md
060d2b6
@JudithBernett
minor changes
1176dc4
@JudithBernett
Merge pull request #14 from picciama/feature/curvecurator_module
f69bf66 
Feature/curvecurator module
@JudithBernett
Update env.yml
ead067a
@JudithBernett
Merge pull request #21 from nf-core/JudithBernett-patch-1
1bd26aa 
Update env.yml
@PascalIversen PascalIversen merged commit b6d27d7 into main Jan 31, 2025
40 of 43 checks passed
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@JudithBernett @PascalIversen @nf-core-bot @picciama