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HighlanderLab
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tree_seq_pipeline
Pipeline to infer tree sequences with different datasets
MIT License
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7
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update inference script
#72
gmafrafortuna
opened
7 months ago
0
More test data and DAG
#71
hannesbecher
closed
8 months ago
1
improve testing
#70
hannesbecher
opened
8 months ago
3
Add tsinfer params to config
#69
hannesbecher
closed
8 months ago
1
Dataset-specific tsinfer params as part of a config file
#68
hannesbecher
closed
8 months ago
1
Devel dont touch data
#67
hannesbecher
closed
8 months ago
1
reproducible testing
#66
hannesbecher
closed
8 months ago
3
Remove print statements
#65
gmafrafortuna
opened
9 months ago
0
updated rule filter (in merge_samples)
#64
gmafrafortuna
opened
9 months ago
0
Basically for the merge rule
#63
gmafrafortuna
closed
9 months ago
0
Change all paths to absolute #52
#62
IsidoreHouaga
closed
8 months ago
3
Move ancestral inferrence after the merge
#61
janaobsteter
opened
9 months ago
0
make `ancestral_Eddie.yaml` easier to adjust
#60
hannesbecher
closed
8 months ago
1
Resolving PR comments
#59
janaobsteter
closed
9 months ago
0
Change all paths to absolute #52
#58
IsidoreHouaga
closed
9 months ago
4
Update README.md - fix correct conda env name
#57
hannesbecher
closed
9 months ago
0
Figure out how to add the pedigree to the inference
#56
janaobsteter
opened
9 months ago
1
Check sgkit documentation how to import a VCF file & how we will move towards using sgkit in this tree seq pipeline
#55
gregorgorjanc
opened
9 months ago
3
Add DAG to README.md #32
#54
gregorgorjanc
closed
8 months ago
1
Update README.md typos
#53
hannesbecher
closed
9 months ago
0
Change all paths to absolute
#52
janaobsteter
closed
8 months ago
2
Adding simlinks and adjusting pipeline to accept input from the ancestral_inference.smk
#51
janaobsteter
closed
9 months ago
0
Add optional arguments to the add_populations function in the Prepare_samples.py
#50
janaobsteter
opened
9 months ago
0
Some rules duplicate vcf files
#49
janaobsteter
closed
9 months ago
1
Recommendations for saving Snakefile and config/cluster files do they don't get overwritten with pulls
#48
janaobsteter
closed
8 months ago
3
How to handle project name?
#47
janaobsteter
closed
9 months ago
0
Modify the ancestral inference to be able to infer on per-chromosome basis
#46
janaobsteter
opened
9 months ago
1
Unify the PROJECT folder name
#45
janaobsteter
closed
9 months ago
1
How to handle files named Chr or chr
#44
janaobsteter
closed
9 months ago
1
Move from samples file constructions to the new sgkit
#43
janaobsteter
opened
9 months ago
1
Add dating scripts to the pipeline
#42
janaobsteter
opened
9 months ago
1
How to handle chromosome names?
#41
janaobsteter
opened
9 months ago
2
Add benchmarking to the rules
#40
janaobsteter
opened
9 months ago
3
Do we need a step to move non-bialellic SNPs from the VCF?
#39
janaobsteter
opened
9 months ago
2
Updates after testing
#38
gmafrafortuna
closed
9 months ago
0
Adding ancestral allele inferrence
#37
janaobsteter
closed
11 months ago
0
The 48h run limit
#36
janaobsteter
closed
11 months ago
1
Find a way to submit snakemake to Eddie
#35
janaobsteter
closed
1 year ago
0
added how to use test data to the README file
#34
gmafrafortuna
closed
10 months ago
0
Add step-by-step instructions on how to get this going into README
#33
gregorgorjanc
closed
1 year ago
0
Add DAG to the README.md
#32
gregorgorjanc
closed
9 months ago
0
Fixed the error with the vcftools log file, cleaned the script, added the log to all the rules
#31
janaobsteter
closed
1 year ago
0
updated tsinfer function, add cluster config
#30
gmafrafortuna
closed
1 year ago
0
How to tell snakemake which one is the "main" file when merging
#29
janaobsteter
opened
1 year ago
0
Adding modules to run on Eddie
#28
janaobsteter
closed
1 year ago
0
Fixing last mistakes
#27
janaobsteter
closed
1 year ago
0
Fixing bugs in the pipeline
#26
janaobsteter
closed
1 year ago
0
Fixing issues and bugs in the pipeline
#25
janaobsteter
closed
1 year ago
0
debugging merging rule
#24
gmafrafortuna
closed
1 year ago
0
Cleaning mistakes
#23
janaobsteter
closed
1 year ago
0
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