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Nextflow #15

Merged
merged 36 commits into from
Apr 30, 2024
Merged

Nextflow #15

merged 36 commits into from
Apr 30, 2024

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jessicaw9910
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Description

Continue NextFlow refactor

Todos

Notable points that this PR has either accomplished or will accomplish.

  • Finalize API clients for cBioPortal, UniProt, Pfam, and KLIFS
  • Refactor cBioPortal code (and any other API clients to make more Pythonic)
  • Get Nextflow running

Questions

  • None

Status

  • In progress

jessicaw9910 and others added 18 commits April 3, 2024 18:02
@jessicaw9910
reformatted cbioportal pipeline for nextflow compatibility
2062134
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
772e94d 
for more information, see https://pre-commit.ci
@jessicaw9910
minor in progress changes in process_cbioportal.nf
685c312
@jessicaw9910
added shebang to process_cbioportal.py
25845a4
@jessicaw9910
updated cbioportal scripts to conform to NF ETL pipeline
a93a19a
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
59b0da4 
for more information, see https://pre-commit.ci
@jessicaw9910
interim commit for transform_cbioportal
e4d2656 
resolved conflicts in cbioportal.py
@jessicaw9910
added transform_cbioportal CLI code
8dbd206
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
c4c8901 
for more information, see https://pre-commit.ci
@jessicaw9910
.gitignore and pyproject.toml changes for transform_cbioportal CLI ch…
57b7237 
…anges
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
29d859d 
for more information, see https://pre-commit.ci
@jessicaw9910
updated NF README
b9c4f56
@jessicaw9910
Merge branch 'main' into nextflow
3deb6d5
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
1e808b1 
for more information, see https://pre-commit.ci
@jessicaw9910
updated cli and pfam scripts
767da80
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
e25f792 
for more information, see https://pre-commit.ci
@jessicaw9910
refactored cbioportal as class instead of functions
3d79381
@jessicaw9910
Merge branch 'main' into nextflow
6ab8658
@codecov Codecov
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codecov bot commented Apr 11, 2024 •
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Codecov Report

Attention: Patch coverage is 0% with 51 lines in your changes are missing coverage. Please review.

Project coverage is 0.68%. Comparing base (a300939) to head (2a24bbe).

❗ Current head 2a24bbe differs from pull request most recent head e237dfb. Consider uploading reports for the commit e237dfb to get more accurate results

Additional details and impacted files

pre-commit-ci bot and others added 11 commits April 11, 2024 14:04
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
2a24bbe 
for more information, see https://pre-commit.ci
@jessicaw9910
separated the extraction of the kinase annotations from the cbioporta…
d508e0b 
…l transform CLI
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
5553f48 
for more information, see https://pre-commit.ci
@jessicaw9910
added poetry to CI.yaml
395c246
@jessicaw9910
tried poetry CI.yaml config alteration from python-poetry/poetry#2629
4b02d97
@jessicaw9910
https://github.com/python-poetry/poetry/issues/5490
587cf43
@jessicaw9910
unmarked proces_cbioportal.nf as an executable
524b01c
@jessicaw9910
reverting by removing SETUPTOOLS_USE_DISTUTILS=stdlib in CI.yaml
21a7fad
@jessicaw9910
commenting out poetry config virtualenvs.create false
eb4a9ea
@jessicaw9910
https://github.com/orgs/python-poetry/discussions/4943
34c7f2a
@jessicaw9910
removed poetry pytest and just running pytest; last fix resolved inst…
43cf473 
…allation errors
@jessicaw9910 jessicaw9910 merged commit f00c721 into main Apr 30, 2024
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