Commits · 77aeb7c4e6d1d0e5c67369658931a726d1442eac · FONDA_A6 / popinSnake · GitLab

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Dec 02, 2024
- 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 6 months ago
  
  f08614ef
- modify notebook input path · f8798e67
  kdc715 authored 6 months ago
  
  f8798e67
- fix bin size consistency across sample analysis · 9f8ed3e1
  kdc715 authored 6 months ago
  
  9f8ed3e1
Oct 16, 2024
- modify coverage analysis output and add samtools environment for coverage analysis · b28f0ec7
  kdc715 authored 6 months ago
  
  b28f0ec7
Oct 08, 2024
- modify coverage calculation method, add analysis for comparing popins filter params and sickle · b0bf1af4
  kdc715 authored 6 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 7 months ago
  
  e04319c9
Feb 28, 2024
- Update references in README.md · c9d25d73
  Birte Kehr authored 1 year ago
  
  c9d25d73
Oct 16, 2023
- Merge branch 'main' of https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake · 915e745c
  kdc715 authored 1 year ago
  
  915e745c
- add VELVET bin · 18fa97a2
  kdc715 authored 1 year ago
  
  18fa97a2
Sep 20, 2023
- change gcc to cxx-compiler; add include ${CONDA_PREFIX} path to sickle compiling · b6cea982
  Kedi Cao authored 1 year ago
  
  b6cea982
Sep 19, 2023
- Update README.md · 760bf216
  Kedi Cao authored 1 year ago
```
remove cmake version
```
  760bf216
Sep 02, 2022
- Merge branch 'main' of https://gitlab.informatik.hu-berlin.de/fonda_a6/popinSnake into main · 14b9c951
  Birte Kehr authored 2 years ago
  
  14b9c951
- Adding example_data/chr21_ins.fa.fai, which is created by the workflow, to the .gitignore file. · d0b4cbb6
  Birte Kehr authored 2 years ago
  
  d0b4cbb6
- Accessing input and output filenames in Jupyter notebooks now via snakemake objects. · c51f3281
  Birte Kehr authored 2 years ago
  
  c51f3281
Sep 01, 2022
- Update README.md with warning that creating conda environments when running... · ea8adf8d
  Birte Kehr authored 2 years ago
```
Update README.md with warning that creating conda environments when running the workflow for the first time may take some time.
```
  ea8adf8d
- Update workflow execution section of README.md (Snakemake requires the --cores... · dba6794c
  Birte Kehr authored 2 years ago
```
Update workflow execution section of README.md (Snakemake requires the --cores parameter to be specified).
```
  dba6794c
- Fixing Nat Genet reference and link to journal in README.md. · 26517aef
  Birte Kehr authored 2 years ago
  
  26517aef
- Adding back popins4snake submodule. · 222d0515
  Birte Kehr authored 2 years ago
  
  222d0515
- Minor update in README.md. · 5e09e05d
  Birte Kehr authored 2 years ago
  
  5e09e05d
- Minor update in README.md. · f09d0358
  Birte Kehr authored 2 years ago
  
  f09d0358
- Resolving conflict in README.md · fe2ae9ea
  Birte Kehr authored 2 years ago
  
  fe2ae9ea
- Removing popins4snake submodule. · 6d2ea9ab
  Birte Kehr authored 2 years ago
  
  6d2ea9ab
- Major revision of README file. · 23c4eba0
  Birte Kehr authored 2 years ago
  
  23c4eba0
- Minor changes to Snakefile and config file. · d038c43f
  Birte Kehr authored 2 years ago
  
  d038c43f
Aug 31, 2022
- Deleting snakemake logs from repository. · b201d894
  Birte Kehr authored 2 years ago
  
  b201d894
Aug 25, 2022
- Adding warning that README.md is outdated. · 1ac02118
  Birte Kehr authored 2 years ago
  
  1ac02118
- Adding updated popins4snake repository as submodule. · 4bb75927
  Birte Kehr authored 2 years ago
  
  4bb75927
- Resolving conflict for config file. · 933f19da
  Birte Kehr authored 2 years ago
  
  933f19da
- Minor change in notebooks to work with current default setup. · b0151f4c
  Birte Kehr authored 2 years ago
  
  b0151f4c
- Cleaning popins4snake location in config file. · ed60b319
  Birte Kehr authored 2 years ago
  
  ed60b319
- Making workflow consistent with new popins4snake version and major cleaning.. · 84e20b3d
  Birte Kehr authored 2 years ago
  
  84e20b3d
- Updating environment for bcftools with version info. · 2e14ef77
  Birte Kehr authored 2 years ago
  
  2e14ef77