HighlanderLab tree_seq_pipeline issues

HighlanderLab / tree_seq_pipeline

Pipeline to infer tree sequences with different datasets

MIT License

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issues

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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