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Feature/curvecurator module #14

Merged
merged 37 commits into from
Jan 30, 2025
Merged

Feature/curvecurator module #14

merged 37 commits into from
Jan 30, 2025

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picciama
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@picciama picciama commented Dec 9, 2024 •
edited by 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 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).

picciama and others added 23 commits November 25, 2024 15:36
@picciama
intermediate commit, added CurveCurator logic
5c8301a
@picciama
Merge branch 'dev' into feature/curvecurator_module
5904671
@picciama
adjusted params for new drevalpy handling
106e497
@picciama
ensured output and task requirements are correct
4793866
@picciama
fixed missing measure arg and fit_curves includes
d353703
@picciama
syntax error fix in call to FIT_CURVES
08cdcc8
@picciama
fix missing comma in call to RUN_CV
82d9193
@picciama
added default measure and fixed arg type
127d72d
@picciama
add missing path_data arg to params_check
df8e42f
@picciama
fix syntax errors and wrong args / file modes
37139c5
@picciama
fixed argument parsing bug
e00b5cb
@picciama
add missing dataset_name arg
67b073c
@picciama
separated fitting into three modules
069e714
@picciama
fixed paths and emits
01b8936
@picciama
fixed publishDirs
e4bd724
@picciama
fixed missing params ref in publishDir
b9f3cf2
@picciama
ensure LOAD_RESPONSE is waiting
befa368
@JudithBernett
fixed path data problems, problem was missing params. in front of pat…
719e2ff 
…h_data in publishDir.
@picciama
created separate preprocessing workflow
b3af48f
@picciama
added missing commas
66bb18b
@JudithBernett
Merge branch 'feature/curvecurator_module' of https://github.com/picc…
4a67fa3 
…iama/drugresponseeval into feature/curvecurator_module
@JudithBernett
giving path_data as value, not as channel, does not work otherwise
98c7800
@JudithBernett
giving back valid measure variables:
674bf15 
if curvecurator&raw -> run processes, if it's curvecurator but already processed, just append _curvecurator to metric, else return normal metric
JudithBernett
JudithBernett approved these changes Dec 10, 2024
View reviewed changes
@JudithBernett JudithBernett reopened this Jan 13, 2025
@JudithBernett JudithBernett linked an issue Jan 29, 2025 that may be closed by this pull request
CurveCurator module #6
Closed
@JudithBernett JudithBernett merged commit f69bf66 into nf-core:dev Jan 30, 2025
6 checks passed
@JudithBernett JudithBernett deleted the feature/curvecurator_module branch January 30, 2025 14:49
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@JudithBernett JudithBernett JudithBernett approved these changes

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CurveCurator module
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@picciama @JudithBernett