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Pairtools manke #1035

Merged
merged 31 commits into from
Aug 13, 2024
Merged

Pairtools manke #1035

merged 31 commits into from
Aug 13, 2024

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thomasmanke
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  • new function plot_DAG() to replace print_DAG()
  • added pytests for makePairs
  • fix conflicitng f-quote in sankePipes.py
  • up python>=3.11
  • retain both --DAG and -v as parallel options
  • commented out a single CI test for scRNAseq --mode STARsolo --> It seems the snakemake reporting is different only for this single instance. Therefore I believe this is related to the checkpoint velocyto and possibly the reporting on tempory files. Compared to a local succesful test, with github action there are additional lines: "Would delete temporary file ..."

@thomasmanke
up python-version in README.rst
e8e5c86
@thomasmanke
add simplified function plot_DAG
4d83282
@thomasmanke
make --DAG and --verbose mutually exclusive arguments
187257f
@thomasmanke
change print_DAG to plot_DAG
dc2d7c5
@thomasmanke
add graphviz dependency to pyproject.toml
1ff4072
@thomasmanke
lint
8cd0483
@thomasmanke
revert exclusive requirement for --DAG and -v. incorporate --verbose=…
d3ecd14 
…False explicitly in plot_DAG()
@thomasmanke
up python-version and remove graphviz as dependency
911869d
@thomasmanke
update README
69f4c2d
@thomasmanke
add TestmakePairs
d9fc4e1
@thomasmanke
fix conflicting string quotes
7708e92
@thomasmanke
fix linting
f77276f
@thomasmanke
bring back graphviz (for now). as not all tools use plot_DAG (yet)
5c5d8e8
@thomasmanke
print info from github actions
0565b84
@thomasmanke
Trying: set timelimit in linux.yml
a62299f
@thomasmanke
WIP: CI testing
2ff76da
@thomasmanke
Merge branch 'pairtools' of github.com:maxplanck-ie/snakepipes into p…
6a2c01c 
…airtools_manke
@thomasmanke
Merge branch 'pairtools_manke' of github.com:maxplanck-ie/snakepipes …
ca94ebd 
…into pairtools_manke
@thomasmanke
WIP: testing. uncomment CI for scRNA
882d28e
@thomasmanke thomasmanke requested a review from WardDeb August 13, 2024 07:59
WardDeb
WardDeb approved these changes Aug 13, 2024
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I've ignored these temp removals systematically now (in ignore pattern), updated line counts and re-enabled the test

@WardDeb
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WardDeb commented Aug 13, 2024

Closes #1032

@thomasmanke thomasmanke merged commit 39848a3 into pairtools Aug 13, 2024
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@WardDeb WardDeb deleted the pairtools_manke branch August 13, 2024 15:00
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@thomasmanke @WardDeb