Feature tutorial - pull new tutorial with example data to master branch #131

LaraFuhrmann · 2022-09-20T08:00:47Z

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…ake version

…eature-benchmark

This reverts commit 94f9e6d.

…tances

…ulation.py

…methods for that

…rain mix

github-actions · 2022-09-23T11:55:34Z

MegaLinter status: ❌ ERROR

Descriptor	Linter	Files	Fixed	Errors	Elapsed time
✅ BASH	shellcheck	8		0	0.21s
❌ MARKDOWN	markdownlint	8	8	5	1.99s
✅ PYTHON	black	41	15	0	3.16s
✅ SNAKEMAKE	snakefmt	21	4	0	11.2s

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This reverts commit d3f52bc. - upstream snakefmt has fixed their bug

kpj and others added 30 commits January 18, 2022 18:24

Add runtime overview plots

dc2cfd4

Dynamically generate conda envs for each job based on job params

7295342

Refactor helper function definitions

2399205

Make dynamically generated conda envs compatible with official Snakem…

0288bea

…ake version

Support PIP packages in dynamically generated conda envs

ec4f44c

Explain dynamic conda env generation in README.md

5b72452

Format shorah_default.py

22adf55

save performance measures also as csv

a9df076

Remove obsolete file

e83f2a1

Set Python version of dynamic conda envs to 3.9

38f1727

compute performance: fixed corner cases

cd0f31b

compute performance: another fix - woopsie

42fb2db

inclusion of new inference method for shorah

b5ba386

Set boost and htslib for dynamic conda envs

94f9e6d

Print method list to stderr

d2f05c9

Merge branch 'feature-benchmark' of github.com:cbg-ethz/V-pipe into f…

01e5db6

…eature-benchmark

Revert "Set boost and htslib for dynamic conda envs"

411ad04

This reverts commit 94f9e6d.

Add boost and htslib dependencies to method scripts

149023c

Format method scripts

2be095f

[Update] update to new shorah_canary version

b0c638a

[Refactor] seperate rules for haplotype generation and read simulation

bafa08a

[Added] Option to simulate haplotype population based on pairwise dis…

218a0f8

…tances

[Added] Option to simulate haplotype population based on pairwise dis…

0ca9860

…tances

[Refactor] shorter column names

f989d2a

[Added] amplicon simulation scheme

d2c8799

[Reformatted] with black

7ce4244

[Added] amplicon simulation scheme

922d3dd

[delete] reads are simulated in amplicon_simulation.py or shotgun_sim…

a654f3b

…ulation.py

[Added] amplicon simulation

3cc740c

[Added] amplicon simulation

e548c8d

Lara Fuhrmann and others added 26 commits July 20, 2022 13:39

[added] lofreq to the benchmark methods

f71fb03

[local_haplotype_setup] config correction

0bdd055

[local_haplotype_setup] correction

f7fb958

correct version

ff01b2e

some updates

a8aeca7

[local_haplotype_setup] added run status

27a8d95

[local_haplotype_setup] correction config

65be0ed

[local_haplotype_setup] correction

53627be

[local_haplotype_setup] change of alpha in shorah method

6be24cf

[local_haplotype_setup] higher memory for realdata setup

0d3d862

[local_haplotype_setup] realdata config

33b6722

[local_haplotype_setup] increase resources for run method

89d38f9

[local_haplotype_setup] config_realdata -- subsampling

0ac299b

[local_haplotype_setup] update methods in config files

759eca5

[local_haplotype_setup] config for long reads

d249e59

[local_haplotype_setup] added amplicon illumina simulaation, adapted …

dbc6413

…methods for that

[local_haplotype_setup] running full benchmark for all configs

7e4bfa2

Use conda function to dynamically generate conda envs

89980b1

Integration of cowwid amplicon benchmarking data

7e67f8f

[local_haplotype_setup] add benchmarking on real data SARS-CoV-2 2-st…

fa3b74e

…rain mix

initial steps for general tutorial

a9acef0

[updated]

3027079

[update+add] added example HIV data, updated tutorial

948bb72

smallcorrections

ea7a1cd

smallcorrections

c205d53

smallcorrections

b1d7638

LaraFuhrmann requested a review from DrYak September 20, 2022 08:00

Revert "Temporary formatting (maybe delete later for easier merging)"

62bad5a

This reverts commit d3f52bc. - upstream snakefmt has fixed their bug

DrYak merged commit e4c0b2f into master Oct 1, 2022

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Feature tutorial - pull new tutorial with example data to master branch #131

Feature tutorial - pull new tutorial with example data to master branch #131

LaraFuhrmann commented Sep 20, 2022

github-actions bot commented Sep 23, 2022 •

edited

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Feature tutorial - pull new tutorial with example data to master branch #131

Feature tutorial - pull new tutorial with example data to master branch #131

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LaraFuhrmann commented Sep 20, 2022

github-actions bot commented Sep 23, 2022 • edited Loading

MegaLinter status: ❌ ERROR

github-actions bot commented Sep 23, 2022 •

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