Skip to content

Commit

Permalink
Fix small mistakes
Browse files Browse the repository at this point in the history
  • Loading branch information
johnbradley committed Mar 8, 2023
1 parent 992e8ea commit 50ec884
Show file tree
Hide file tree
Showing 2 changed files with 4 additions and 6 deletions.
8 changes: 3 additions & 5 deletions episodes/01_introduction.md
Original file line number Diff line number Diff line change
Expand Up @@ -23,20 +23,18 @@ teaching: 10
- Scalable
- Reusable

## Strengths and Weaknesses of Snakemake

## Strengths
## Strengths of Snakemake
- Only creates missing or out of date files
- Flexible control over which files are created
- Uses potentially familiar Python syntax
- Dynamic branching - Output files and commands used determined while the workflow is running

## Weaknesses
## Weaknesses of Snakemake
- Rule based logic instead of procedural logic
- Requires some python code/knowledge for typical workflows

## Class Plan
- Create Snakemake Workflow that
- Runs R scripts for filtering and final analysis
- Runs Machine Learning Components
- Efficently processes many files at the same time
- Efficiently processes many files at the same time
2 changes: 1 addition & 1 deletion episodes/05_setup_env.md
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ This module will switch Compiler environment to gnu/11.2.0 and load mkl/2021.3.0
Lmod is automatically replacing "intel/19.0.5" with "gnu/11.2.0".
The following have been reloaded with a version change:
1) mvapich2/2.3.3 => mvapich2/2.3.6
Configuring R to use the yaml, dplyr, and rmarkdown packages.
Configuring R to use the yaml package.
Configuring singularity to use a cache to speed up pulling containers.
```

Expand Down

0 comments on commit 50ec884

Please sign in to comment.