karel-brinda / MiniPhy

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

https://brinda.eu/mof

karel-brinda/MiniPhy Issues

Add possibility to pass cluster params
Closed 4 months ago
Tree inference – argument list too long: '/bin/sh
Closed 4 months ago
Resume jobs
Closed 4 months ago3
Extend documentation in the readme
Updated 4 months ago
Remove pandas & numpy as dependencies
Updated 4 months ago1
Remove ete3 dependency
Updated 4 months ago1
ProPhyle-based compression failing – but only with certain versions of Snakemake
Closed 4 months ago8
Missing int conversion by argparse in `create_batches.py`
Closed 4 months ago2
Add detailed batch stats (for individual samples/records)
Updated 4 months ago1
Dont use dirs as outputs
Updated 4 months ago1
Add an option for tree post-processing (to switch it off)
Updated 4 months ago
Enhancement: do all the `seqtk seq` file conversion at once, parallelized eg by GNU parallel
Updated 4 months ago
Suggestion on create_batches.py
Updated 4 months ago1
Dustbin creation – iterate over species in their alphabetical order
Closed 4 months ago
Add a param for adding comments to batching output text files
Closed 4 months ago
Add a default script for batching
Closed 4 months ago
snakemake.workflow.srcdir discontinued in new versions of Snakemake
Closed 4 months ago4
Missing dependency: grpc
Closed 4 months ago6
Simplify testing
Closed 4 months ago
Add number of snakemake threads to config
Closed 4 months ago
Add detailed batch stats
Closed 8 months ago1
Add an option to fail if tree is not provided
Closed 8 months ago
Make jellyfish more configurable
Closed 8 months ago
Tests not runnable by `make` from `.test`
Closed 8 months ago
Add a make subcommand for just re-compressing the final files
Closed 8 months ago
Release and include a new version of ProPhyle with propagation without BWT
Closed 8 months ago
Config options are parsed only on the top level yaml
Closed 8 months ago
Update docs after the update of the pipeline
Closed 8 months ago
Add newick to post output
Closed 8 months ago
Input files should be relative to the list of files
Closed 8 months ago2
merge_global_stats.py: error: the following arguments are required: batch.global.stats
Closed 8 months ago1
Add param to config indicating whether Snakemake should use conda
Closed 8 months ago1
Make xz compression configurable
Closed 8 months ago
Split results to results and intermediate
Closed 8 months ago
Show filename in case of the "Unknown suffix" error
Closed 8 months ago1
Support properly dir outputs
Closed 8 months ago3
MissingInputException: Missing input files for rule symlink_nw_tree
Closed 8 months ago1
Underscores in file names confuse the pipeline
Closed 8 months ago1
Choice between txt (simpl) and fa as a configuration param
Closed 8 months ago1
Input gz decompression doesn't work
Closed 8 months ago1
K-mer counting should use only 1 snakemake thread and max number of cores
Closed 8 months ago8
Add configuration
Closed 8 months ago1
ModuleNotFoundError: No module named 'ete3'
Closed 8 months ago
Conda: avoid duplicating package downloads for test vs non-test
Closed 8 months ago
Add 'make conda' for just building all conda envs
Closed 8 months ago
Add a possibility of using custom trees
Closed 3 years ago
Add file sizes to the output stats
Closed 3 years ago
In dry run (-n), Snakemake is trying to load the node list before it exists
Closed 3 years ago1
Post-propagation input files resolved incorrectly
Closed 3 years ago1
Always use binary tree with a root
Closed 3 years ago