Commits · 32c4aa8ec1443e5c8b00855ca20d09efca571783 · FONDA_A6 / popinSnake

Mar 14, 2025
- change .png extensions to .pdf, add empty samples list in config · 32c4aa8e
  Kedi Cao authored 3 weeks ago
  
  32c4aa8e
Mar 04, 2025
- clear notebook output · ccd96b4c
  Kedi Cao authored 1 month ago
  
  ccd96b4c
- re-arrange rules · 0b5ebc9d
  Kedi Cao authored 1 month ago
  
  0b5ebc9d
- save notebook analysis in .txt and .pdf format · 0edb88a1
  Kedi Cao authored 1 month ago
  
  0edb88a1
Feb 21, 2025

workflow can either automatically detect sample · e03b0e22

kdc715 authored 1 month ago

s from input_dir or analyze only provided samples from the config file;conda default channel deprecated;add logging for python script

e03b0e22

Feb 13, 2025
- fix analysis after contamination removal · 3631fcbf
  kdc715 authored 1 month ago
  
  3631fcbf
Jan 30, 2025
- remove temporary files from rule_all, add input files missing for genotype rule · 40d3d502
  kdc715 authored 2 months ago
  
  40d3d502
- add more temporary files to be removed when workflow finish · 49083683
  kdc715 authored 2 months ago
  
  49083683
Jan 27, 2025
- remove chromosome info from coverage analysis, only keep contigs · 4dcf79b4
  kdc715 authored 2 months ago
  
  4dcf79b4
Jan 23, 2025
- samtools multithreading scheduling fix · f30daff1
  kdc715 authored 2 months ago
  
  f30daff1
Jan 21, 2025
- fix memory allocation for samtool multithreading rules · 021311d9
  kdc715 authored 2 months ago
  
  021311d9
- fix file paths missing / in jupyter notebook · 4c04a11b
  kdc715 authored 2 months ago
  
  4c04a11b
Dec 18, 2024
- remove kraken memory mapping for slurm · 58e5ae2d
  kdc715 authored 3 months ago
  
  58e5ae2d
- fixing filepaths for conda environment paths, notebook paths, and notebook inputs · b06c0523
  kdc715 authored 3 months ago
  
  b06c0523
Dec 17, 2024
- modify resource parameters from time to runtime, value 12:00:00 to 12h · fa5048ec
  kdc715 authored 3 months ago
  
  fa5048ec
- fix path error for notebook analysis outputs · d1f30f60
  kdc715 authored 3 months ago
  
  d1f30f60
Dec 16, 2024
- fix snakemake wildcard error for log file · 5ba6e0c4
  kdc715 authored 3 months ago
  
  5ba6e0c4
- change default email waiting time to 12:00:00 to be consistent with the group schedualing time · 5e3ed3c7
  kdc715 authored 3 months ago
  
  5e3ed3c7
- fix log files; change email waiting time to 12:00:00 · b68c11c9
  kdc715 authored 3 months ago
  
  b68c11c9
Dec 13, 2024
- fix resources for dynamic scheduling · a5062978
  kdc715 authored 3 months ago
  
  a5062978
- fix file path for python script · ced99c46
  kdc715 authored 3 months ago
  
  ced99c46
- add dynamic scheduling for crop_unmapped · 1338cbbf
  kdc715 authored 3 months ago
  
  1338cbbf
Dec 12, 2024
- add cluster configuration for all rules, update README, remove manual input for sample names · 0ace4544
  kdc715 authored 3 months ago
  
  0ace4544
Dec 10, 2024
- fix binary paths, rename git submodule · 2eba2544
  Kedi Cao authored 3 months ago
  
  2eba2544
Dec 05, 2024
- fix wokrflow_path of python script · d66867ec
  Kedi Cao authored 3 months ago
  
  d66867ec
Dec 02, 2024
- add option to turn on and off email notifications · c78ae311
  Kedi Cao authored 4 months ago
  
  c78ae311
- fix path for kraken_db specification · 77aeb7c4
  Kedi Cao authored 4 months ago
  
  77aeb7c4
- add ability to send user email notifications before jupyter notebook... · d8839d96
  Kedi Cao authored 4 months ago
```
add ability to send user email notifications before jupyter notebook execution; fix workflow_path issues
```
  d8839d96
Nov 29, 2024
- modify config paths · 4cab4fc3
  Kedi Cao authored 4 months ago
  
  4cab4fc3
- rename modules; seperate output paths and workflow paths · 04f162d0
  Kedi Cao authored 4 months ago
  
  04f162d0
Oct 25, 2024
- add read numbers analysis for after kraken with no sickle filtering · aae16ed0
  kdc715 authored 5 months ago
  
  aae16ed0
Oct 21, 2024
- resolve issue with coverage input for find_location rule when analysis parameter is turned off · f08614ef
  kdc715 authored 5 months ago
  
  f08614ef
- modify notebook input path · f8798e67
  kdc715 authored 5 months ago
  
  f8798e67
- fix bin size consistency across sample analysis · 9f8ed3e1
  kdc715 authored 5 months ago
  
  9f8ed3e1
Oct 16, 2024
- modify coverage analysis output and add samtools environment for coverage analysis · b28f0ec7
  kdc715 authored 5 months ago
  
  b28f0ec7
Oct 08, 2024
- modify coverage calculation method, add analysis for comparing popins filter params and sickle · b0bf1af4
  kdc715 authored 5 months ago
  
  b0bf1af4
Oct 02, 2024
- use samtools to calculate contig coverage and change notebook for heatmap visualization · 71d33b17
  kdc715 authored 6 months ago
  
  71d33b17
Sep 30, 2024
- modify snakefiles to add log files and benchmarking options for each rule · e004f263
  kdc715 authored 6 months ago
  
  e004f263
Sep 27, 2024
- fix analysis module, clean up jupyter notebook functions · 25c4367f
  kdc715 authored 6 months ago
  
  25c4367f
Sep 23, 2024
- add modularized workflow with kraken2 for contamination removal to new branch for testing · e04319c9
  kdc715 authored 6 months ago
  
  e04319c9