Improve snakemake mindset

Author: johnbradley

episodes/02_snakemake_mindset.md

@@ -8,6 +8,7 @@ teaching: 10
 - What are the parts of a snakemake workflow?
 - What is a snakemake rule?
 - How does snakemake combine rules into jobs to run?
+- How is a Snakemake Rule different from a Snakemake Job?
 
 ::::::::::::::::::::::::::::::::::::::::::::::::
 ::::::::::::::::::::::::::::::::::::: objectives
@@ -25,9 +26,6 @@ teaching: 10
 - Provides support for specifying containers for each rule
 - Provides support for many HPC Clusters including SLURM
 
-TODO
-Explain DAG
-
 ## What is a Snakemake Rule?
 
 Main parts of a Snakemake Rule used in this workshop
@@ -51,6 +49,31 @@ rule <name>:
 ```
 
 ## How Snakemake combines rules
+### Example workflow
+
+Create checksums for each image and zip up the results
+```
+fish1.jpg
+fish2.jpg
+```
+rule checksum1:
+    input: "fish1.jpg"
+    output: "fish1.checksum"
+    ...
+   
+rule checksum2:
+    input: "fish2.jpg"
+    output: "fish2.checksum"   
+    ...
+   
+rule zip:
+    input: "fish1.jpg", "fish1.checksum", "fish2.jpg", "fish2.checksum"
+    ouput: "result.zip"
+    ...
+```
+
+Explain DAG
+DAG (directed acyclic graph) 
 
 Rules vs Jobs
 Job is running a rule to create a specific set of output files.

episodes/12_run_on_slurm.md

@@ -55,7 +55,7 @@ Create a script name `run-workflow.sh` to run snakemake in the background.
 #SBATCH --time=00:30:00
 . Scripts/setup_env.sh
 JOBS=10
-snakemake --jobs $JOBS --use-singularity --profile slurm/ "$@"
+snakemake --jobs $JOBS --use-singularity --profile slurm/
 ```
 
 ## Delete All Outputs
@@ -66,7 +66,7 @@ snakemake c1 --delete-all-output
 ## Run Background job and monitor progress
 Run snakemake in the background scaling up
 ```bash
-sbatch run-workflow.sh -c10
+sbatch run-workflow.sh
 ```
 
 ## Monitor job
@@ -78,6 +78,5 @@ squeue -u $LOGNAME
 
 Where did my logs go?
 ```bash
-ls logs
 ls logs/
 ```