cg

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cg stands for Clinical Genomics; a clinical sequencing platform under SciLifeLab

In this context, cg provides the interface between these tools to facilitate automation and other necessary cross-talk. It also exposes some APIs:

Contributing

Please check out our guide for contributing to cg

Installation

Cg written in Python 3.9+ and is available on the Python Package Index (PyPI).

pip install cg

If you would like to install the latest development version, use poetry.

git clone https://github.com/Clinical-Genomics/cg
cd cg
poetry install

For development, use poetry install --all-extras to install development dependencies.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (88.3.0)

3 maintainers

PyPI data
Data sourced directly from PyPI's database.
Avatar for clingen from gravatar.com clingen Avatar for karlnyr from gravatar.com karlnyr Avatar for Vince-janv from gravatar.com Vince-janv

Requires

Python <3.13, >=3.11

Provides Extra

coveralls mock pre-commit pytest pytest-cov pytest-freezegun pytest-httpserver pytest-mock pytest-xdist ruff

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

cg-87.10.2.tar.gz (703.2 kB view details)

Uploaded Source

Built Distribution

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cg-87.10.2-py3-none-any.whl (1.1 MB view details)

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  • Upload date:
  • Size: 1.1 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: poetry/2.4.1 CPython/3.11.15 Linux/6.17.0-1020-azure

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Release history Release notifications | RSS feed

88.3.0

88.2.5

88.2.4

88.2.3

88.2.2

88.2.1

88.2.0

88.1.5

88.1.4

88.1.3

88.1.2

88.1.1

88.1.0

88.0.3

88.0.2

88.0.1

88.0.0

87.10.3

This release

87.10.2

87.10.1

87.10.0

87.9.5

87.9.4

87.9.3

87.9.2

87.9.1

87.9.0

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55.4.6

55.4.5

55.4.4

55.4.3

55.4.2

55.4.1

55.4.0

55.3.10

55.3.9

55.3.8

55.3.7

55.3.6

55.3.5

55.3.4

55.3.3

55.3.2

55.3.1

55.3.0

55.2.3

55.2.2

55.2.1

55.2.0

55.1.1

55.1.0

55.0.0

54.10.7

54.10.6

54.10.5

54.10.4

54.10.3

54.10.2

54.10.1

54.10.0

54.9.1

54.9.0

54.7.0

54.6.1

54.6.0

54.5.3

54.5.2

54.5.1

54.5.0

54.4.10

54.4.9

54.4.8

54.4.7

54.4.6

54.4.5

54.4.4

54.4.3

54.4.2

54.4.1

54.4.0

54.3.1

54.3.0

54.2.1

54.2.0

54.1.3

54.1.2

54.1.1

54.1.0

54.0.0

53.6.0

53.5.4

53.5.3

53.5.2

53.5.1

53.5.0

53.4.8

53.4.7

53.4.6

53.4.5

53.4.4

53.4.3

53.4.2

53.4.1

53.4.0

53.3.0

53.2.0

53.1.11

53.1.10

53.1.9

53.1.8

53.1.7

53.1.6

53.1.5

53.1.4

53.1.3

53.1.2

53.1.1

53.1.0

53.0.2

53.0.1

53.0.0

52.1.6

52.1.5

52.1.4

52.1.3

52.1.2

52.1.1

52.1.0

52.0.11

52.0.10

52.0.9

52.0.8

52.0.7

52.0.6

52.0.5

52.0.4

52.0.3

52.0.2

52.0.1

52.0.0

51.10.7

51.10.6

51.10.5

51.10.4

51.10.3

51.10.2

51.10.1

51.10.0

51.9.10

51.9.8

51.9.7

51.9.6

51.9.5

51.9.4

51.9.3

51.9.2

51.9.1

51.9.0

51.8.1

51.8.0

51.7.6

51.7.5

51.7.4

51.7.3

51.7.2

51.7.1

51.7.0

51.6.14

51.6.13

51.6.12

51.6.11

51.6.10

51.6.9

51.6.8

51.6.7

51.6.6

51.6.5

51.6.4

51.6.3

51.6.2

51.6.1

51.6.0

51.5.15

51.5.14

51.5.13

51.5.12

51.5.11

51.5.10

51.5.9

51.5.8

51.5.7

51.5.6

51.5.5

51.5.4

51.5.3

51.5.2

51.5.1

51.4.1

51.4.0

51.3.1

51.3.0

51.2.9

51.2.8

51.2.7

51.2.6

51.2.5

51.2.4

51.2.3

51.2.2

51.2.1

51.2.0

51.1.3

51.1.2

51.1.1

51.1.0

51.0.9

51.0.8

51.0.7

51.0.6

51.0.5

51.0.4

51.0.3

51.0.2

51.0.1

51.0.0

50.1.10

50.1.9

50.1.8

50.1.7

50.1.6

50.1.5

50.1.4

50.1.3

50.1.2

50.1.1

50.1.0

50.0.0

49.5.2

49.5.1

49.5.0

49.4.7

49.4.6

49.4.5

49.4.4

49.4.3

49.4.2

49.4.1

49.4.0

49.3.0

49.2.0

49.1.0

49.0.16

49.0.14

49.0.13

49.0.12

49.0.11

49.0.10

49.0.9

49.0.8

49.0.7

49.0.6

49.0.5

49.0.4

49.0.3

49.0.2

49.0.1

49.0.0

48.0.0

47.0.1

47.0.0

46.0.5

46.0.4

46.0.3

46.0.2

46.0.1

46.0.0

45.5.5

45.5.4

45.5.3

45.5.2

45.5.1

45.5.0

45.4.5

45.4.4

45.4.3

45.4.2

45.4.1

45.4.0

45.3.0

45.2.2

45.2.1

45.2.0

45.1.3

45.1.2

45.1.1

45.1.0

45.0.17

45.0.16

45.0.15

45.0.14

45.0.13

45.0.12

45.0.11

45.0.10

45.0.9

45.0.8

45.0.7

45.0.6

45.0.5

45.0.4

45.0.3

45.0.2

45.0.1

45.0.0

44.0.5

44.0.4

44.0.3

44.0.2

44.0.1

44.0.0

43.0.5

43.0.4

43.0.3

43.0.2

43.0.1

43.0.0

42.0.0

41.0.2

41.0.1

41.0.0

40.12.4

40.12.3

40.12.2

40.12.1

40.12.0

40.11.1

40.11.0

40.10.1

40.10.0

40.9.7

40.9.6

40.9.5

40.9.4

40.9.2

40.9.1

40.8.2

40.8.1

40.7.1

40.7.0

40.6.3

40.6.2

40.6.1

40.6.0

40.5.1

40.5.0

40.4.1

40.4.0

40.3.3

40.3.2

40.3.1

40.3.0

40.2.3

40.2.2

40.2.1

40.2.0

40.1.5

40.1.4

40.1.3

40.1.2

40.1.1

40.1.0

40.0.1

40.0.0

39.1.0

39.0.0

38.3.5

38.3.4

38.3.3

38.3.2

38.3.1

38.3.0

38.2.10

38.2.9

38.2.8

38.2.7

38.2.6

38.2.5

38.2.4

38.2.3

38.2.2

38.2.1

38.2.0

38.1.9

38.1.8

38.1.7

38.1.6

38.1.5

38.1.4

38.1.3

38.1.2

38.1.1

38.1.0

38.0.2

38.0.1

38.0.0

37.2.0

37.1.0

37.0.28

37.0.26

37.0.25

37.0.24

37.0.23

37.0.22

37.0.21

37.0.20

37.0.17

37.0.16

37.0.15

37.0.14

37.0.13

37.0.12

37.0.11

37.0.10

37.0.9

37.0.8

37.0.7

37.0.6

37.0.5

37.0.4

37.0.3

37.0.2

37.0.1

37.0.0

36.5.1

36.5.0

36.4.2

36.4.1

36.4.0

36.3.2

36.3.1

36.3.0

36.2.7

36.2.6

36.2.5

36.2.4

36.2.3

36.2.2

36.2.1

36.1.0

36.0.4

36.0.3

36.0.2

36.0.1

35.0.2

35.0.1

34.0.0

33.3.4

33.3.3

33.3.2

33.3.1

33.3.0

33.2.3

33.2.1

33.2.0

33.1.6

33.1.5

33.1.4

33.1.3

33.1.2

33.1.1

33.1.0

33.0.6

33.0.5

33.0.4

33.0.3

33.0.2

33.0.1

33.0.0

32.2.8

32.2.7

32.2.5

32.2.4

32.2.3

32.2.2

32.2.1

32.2.0

32.1.0

32.0.0

31.2.3

31.2.2

31.2.1

31.2.0

31.1.6

31.1.5

31.1.4

31.1.3

31.1.2

31.1.0

31.0.2

31.0.1

31.0.0

30.3.0

30.2.7

30.2.6

30.2.4

30.2.3

30.2.2

30.2.0

30.1.4

30.1.2

30.1.1

30.1.0

30.0.0

29.8.7

29.8.6

29.8.5

29.8.4

29.8.3

29.8.2

29.8.1

29.8.0

29.7.1

29.7.0

29.6.0

29.5.7

29.5.6

29.5.5

29.5.4

29.5.3

29.5.2

29.5.1

29.5.0

29.4.13

29.4.12

29.4.11

29.4.10

29.4.9

29.4.8

29.4.7

29.4.6

29.4.5

29.4.4

29.4.3

29.4.2

29.4.1

29.4.0

29.3.1

29.3.0

29.2.0

29.1.7

29.1.6

29.1.5

29.1.4

29.1.3

29.1.2

29.1.1

29.1.0

29.0.3

29.0.2

29.0.1

29.0.0

28.0.5

28.0.4

28.0.3

28.0.2

28.0.1

28.0.0

27.3.13

27.3.12

27.3.11

27.3.10

27.3.9

27.3.8

27.3.7

27.3.5

27.3.4

27.3.3

27.3.2

27.3.1

27.3.0

27.2.15

27.2.14

27.2.13

27.2.12

27.2.11

27.2.10

27.2.9

27.2.8

27.2.7

27.2.6

27.2.5

27.2.4

27.2.3

27.2.2

27.2.1

27.2.0

27.1.64

27.1.62

27.1.61

27.1.60

27.1.59

27.1.58

27.1.57

27.1.56

27.1.55

27.1.53

27.1.52

27.1.51

27.1.50

27.1.49

27.1.48

27.1.47

27.1.46

27.1.45

27.1.44

27.1.43

27.1.42

27.1.41

27.1.40

27.1.39

27.1.38

27.1.37

27.1.36

27.1.35

27.1.34

27.1.33

27.1.32

27.1.31

27.1.30

27.1.29

27.1.28

27.1.26

27.1.25

27.1.24

27.1.23

27.1.22

27.1.21

27.1.20

27.1.19

27.1.18

27.1.17

27.1.16

27.1.15

27.1.14

27.1.13

27.1.12

27.1.11

27.1.10

27.1.9

27.1.8

27.1.7

27.1.6

27.1.5

27.1.4

27.1.3

27.1.2

27.1.1

27.0.11

27.0.10

27.0.8

27.0.7

27.0.6

27.0.5

27.0.4

27.0.3

27.0.2

27.0.1

27.0.0

26.7.5

26.7.4

26.7.3

26.7.2

26.7.1

26.7.0

26.6.3

26.6.2

26.6.1

26.6.0

26.5.1

26.5.0

26.4.3

26.4.2

26.4.1

26.4.0

26.3.5

26.3.4

26.3.3

26.3.2

26.3.1

26.3.0

26.2.1

26.2.0

26.1.2

26.1.1

26.1.0

26.0.9

26.0.8

26.0.7

26.0.6

26.0.5

26.0.4

26.0.3

26.0.2

26.0.1

26.0.0

25.3.0

25.2.2

25.2.1

25.2.0

25.1.0

25.0.0

24.1.1

24.1.0

24.0.9

24.0.8

24.0.7

24.0.6

24.0.5

24.0.3

24.0.2

24.0.1

24.0.0

23.8.2

23.8.1

23.8.0

23.7.3

23.7.2

23.7.1

23.7.0

23.6.4

23.6.3

23.6.2

23.6.1

23.6.0

23.5.0

23.4.0

23.3.6

23.3.5

23.3.4

23.3.3

23.3.1

23.3.0

23.2.6

23.2.5

23.2.4

23.2.3

23.2.2

23.2.0

23.1.1

23.1.0

23.0.0

22.91.0

22.90.3

22.90.2

22.90.1

22.90.0

22.89.2

22.89.1

22.89.0

22.88.0

22.87.0

22.86.0

22.85.6

22.85.5

22.85.4

22.85.3

22.85.2

22.85.1

22.85.0

22.84.6

22.84.5

22.84.4

22.84.3

22.84.2

22.84.1

22.84.0

22.83.1

22.83.0

22.82.0

22.81.5

22.81.4

22.81.3

22.81.2

22.81.1

22.81.0

22.80.1

22.80.0

22.79.1

22.79.0

22.78.9

22.78.8

22.78.7

22.78.6

22.78.5

22.78.4

22.78.3

22.78.2

22.78.1

22.78.0

22.77.2

22.77.1

22.76.1

22.76.0

22.75.5

22.75.4

22.75.3

22.75.2

22.75.1

22.75.0

22.74.1

22.74.0

22.73.0

22.72.0

22.71.1

22.71.0

22.70.1

22.70.0

22.69.0

22.68.0

22.67.1

22.67.0

22.66.0

22.65.1

22.65.0

22.64.0

22.63.3

22.63.2

22.63.1

22.63.0

22.62.3

22.62.2

22.62.0

22.61.5

22.61.4

22.61.3

22.61.2

22.61.1

22.61.0

22.60.0

22.59.0

22.58.0

22.57.5

22.57.4

22.57.3

22.57.2

22.57.0

22.56.3

22.56.2

22.56.1

22.56.0

22.55.1

22.55.0

22.54.12

22.54.11

22.54.10

22.54.9

22.54.7

22.54.6

22.54.5

22.54.4

22.54.3

22.54.2

22.54.1

22.54.0

22.53.0

22.52.0

22.51.0

22.50.0

22.49.2

22.49.1

22.49.0

22.48.1

22.48.0

22.47.1

22.47.0

22.46.6

22.46.5

22.46.4

22.46.3

22.46.2

22.46.1

22.46.0

22.45.0

22.44.5

22.44.4

22.44.3

22.44.2

22.44.1

22.44.0

22.43.2

22.43.1

22.43.0

22.42.0

22.41.3

22.41.2

22.41.1

22.41.0

22.40.5

22.40.4

22.40.3

22.40.2

22.40.1

22.39.1

22.39.0

22.38.3

22.38.2

22.38.1

22.38.0

22.37.4

22.37.3

22.37.2

22.37.0

22.36.1

22.36.0

22.35.0

22.34.4

22.34.3

22.34.2

22.34.1

22.34.0

22.33.0

22.32.2

22.32.1

22.32.0

22.31.7

22.31.6

22.31.5

22.31.4

22.31.3

22.31.2

22.31.1

22.31.0

22.30.0

22.29.3

22.29.2

22.29.1

22.29.0

22.28.0

22.27.0

22.26.0

22.25.6

22.25.5

22.25.4

22.25.3

22.25.2

22.25.1

22.24.1

22.24.0

22.23.2

22.23.1

22.23.0

22.22.0

22.21.1

22.21.0

22.20.1

22.20.0

22.19.8

22.19.7

22.19.6

22.19.5

22.19.4

22.19.3

22.19.2

22.19.1

22.19.0

22.18.0

22.17.2

22.17.1

22.17.0

22.16.0

22.15.0

22.14.0

22.13.0

22.12.0

22.11.2

22.11.1

22.10.3

22.10.2

22.10.1

22.10.0

22.9.4

22.9.3

22.9.2

22.9.1

22.9.0

22.8.6

22.8.5

22.8.4

22.8.3

22.8.2

22.8.1

22.8.0

22.7.0

22.6.1

22.6.0

22.5.2

22.5.1

22.5.0

22.4.1

22.4.0

22.3.1

22.3.0

22.2.2

22.2.1

22.2.0

22.1.3

22.1.2

22.1.1

22.1.0

22.0.1

22.0.0

21.13.0

21.12.2

21.12.1

21.12.0

21.11.0

21.10.0

21.9.3

21.9.2

21.9.1

21.9.0

21.8.3

21.8.2

21.8.1

21.8.0

21.7.2

21.7.1

21.7.0

21.6.9

21.6.8

21.6.7

21.6.6

21.6.5

21.6.4

21.6.3

21.6.2

21.6.1

21.6.0

21.5.7

21.5.6

21.5.5

21.5.4

21.5.3

21.5.2

21.5.1

21.5.0

21.4.4

21.4.3

21.4.2

21.4.1

21.4.0

21.3.1

21.3.0

21.2.0

21.1.0

21.0.0

20.26.2

20.26.1

20.26.0

20.25.0

20.24.0

20.23.0

20.22.0

20.21.1

20.21.0

20.20.1

20.20.0

20.19.5

20.19.4

20.19.3

20.19.2

20.19.1

20.19.0

20.18.0

20.17.5

20.17.4

20.17.3

20.17.2

20.17.1

20.17.0

20.16.0

20.15.1

20.15.0

20.14.2

20.14.1

20.14.0

20.13.0

20.12.1

20.12.0

20.11.0

20.10.1

20.10.0

20.9.12

20.9.11

20.9.10

20.9.9

20.9.8

20.9.7

20.9.6

20.9.5

20.9.3

20.9.2

20.9.1

20.9.0

20.8.1

20.8.0

20.7.0

20.6.0

20.5.4

20.5.3

20.5.2

20.5.1

20.5.0

20.4.0

20.3.3

20.3.2

20.3.1

20.3.0

20.2.1

20.2.0

20.1.4

20.1.3

20.1.2

20.1.1

20.1.0

20.0.1

20.0.0

19.5.4

19.5.3

19.5.2

19.5.1

19.5.0

19.4.0

19.3.2

19.3.1

19.3.0

19.2.0

19.1.1

19.1.0

19.0.0

18.12.1

18.12.0

18.11.4

18.11.3

18.11.2

18.11.1

18.11.0

18.10.2

18.10.1

18.10.0

18.9.1

18.9.0

18.8.0

18.7.2

18.7.1

18.7.0

18.6.0

18.5.1

18.5.0

18.4.0

18.3.0

18.2.0

18.1.5

18.1.4

18.1.3

18.1.2

18.1.1

18.1.0

18.0.0

17.2.1

17.2.0

17.1.0

17.0.0

16.17.1

16.17.0

16.16.1

16.16.0

16.15.1

16.15.0

16.14.0

16.13.0

16.12.1

16.12.0

16.11.1

16.11.0

16.10.4

16.10.3

16.10.2

16.10.1

16.10.0

16.9.0

16.8.1

16.8.0

16.7.1

16.7.0

16.6.0

16.5.0

16.4.3

16.4.2

16.4.1

16.4.0

16.3.4

16.3.3

16.3.2

16.3.1

16.3.0

16.2.0

16.1.1

16.1.0

16.0.6

16.0.5

16.0.4

16.0.3

16.0.2

16.0.1

16.0.0

15.0.4

15.0.3

15.0.2

15.0.1

15.0.0

14.0.1

14.0.0

13.18.0

13.17.2

13.17.1

13.17.0

13.16.2

13.16.1

13.16.0

13.15.0

13.14.3

13.14.2

13.14.1

13.14.0

13.13.0

13.12.1

13.12.0

13.11.0

13.10.1

13.10.0

13.9.0

13.8.0

13.7.0

13.6.0

13.5.0

13.4.1

13.4.0

13.3.1

13.3.0

13.2.0

13.1.0

13.0.0

12.7.1

12.7.0

12.6.0

12.5.0

12.4.0

12.3.6

12.3.5

12.3.4

12.3.3

12.3.2

12.3.1

12.3.0

12.2.0

12.1.7

12.1.6

12.1.5

12.1.4

12.1.3

1.0.0

1.0.0b2 pre-release

0.9.1

0.9.0

Supported by

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