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Updates to the pipeline #11

Merged
merged 32 commits into from
Aug 10, 2023
Merged

Updates to the pipeline #11

merged 32 commits into from
Aug 10, 2023

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SaimMomin12
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Recent Changes to the pipeline:

  • Added Kraken2 Heatmap Plot
  • Updated README
    • Information about output files tree
    • Setting up Synapse Configuration file
    • Input Samplesheet schema for SRA and Synapse Analysis mode
  • Minor architectural updates to the pipeline.
  • More Structured and generalized config.yaml file
  • Other Minor Changes as per Issues

Saim Momin and others added 30 commits March 6, 2023 15:32
Cleanup
791b771
Initial Commit
a69e97b
@SaimMomin12
Update README.md
e8805bc
@SaimMomin12
Updated Framework of Pipeline
f41d9a3
@SaimMomin12
Minor changes
472631b
@SaimMomin12
Purged rules
926f86c
@SaimMomin12
Added script for Kraken2 Plots
6cad1c3
@SaimMomin12
Added Synapse ID fetching script
793ab57
@SaimMomin12
Snakemake rules and ReadME updation
480f8d9
@SaimMomin12
Added Flake workflow
0746ed4
@SaimMomin12
Updated flake.yml
9ccd0a4
@SaimMomin12
Updated flake.yml
67afd96
@SaimMomin12
Updated flake.yml
37a0d06
@SaimMomin12
Updated flake.yml
90aa6de
@SaimMomin12
Added linting
50e9391
@SaimMomin12
Pipeline Cleanup
5845a9d
@SaimMomin12
Update flake.yml
97a5ca4
@SaimMomin12
Update README.md
8c9be2c
@SaimMomin12
Code Cleanup
884e851
@SaimMomin12
Merge branch 'dev' of github.com:maxplanck-ie/sc-virome-scan into dev
e77e824
@SaimMomin12
Code Cleanup
5eb0359
@SaimMomin12
Updated Cellranger rule
965aef8
@SaimMomin12
Minor Changes to Script
299eaf3
@SaimMomin12
Minor Changes
0337b71
@SaimMomin12
Code Cleanup
e302a81
@SaimMomin12
Added Synpase Integration with pipeline
be49978
@SaimMomin12
Added Synapse requirement in env.yaml
3230f71
@SaimMomin12
Update README.md
8b3d139
@SaimMomin12
Update README.md
31d46ff
@WardDeb
Merge pull request #2 from maxplanck-ie/dev
32a2895 
Minor Changes to the pipeline
@SaimMomin12 SaimMomin12 merged commit fb71b2a into main Aug 10, 2023
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@WardDeb WardDeb WardDeb approved these changes

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@SaimMomin12 @WardDeb