From 2ff9d953357d319e02b4dfe5fe3ff4863d011c2a Mon Sep 17 00:00:00 2001
From: John Bradley <johnbradley2008@gmail.com>
Date: Wed, 8 Mar 2023 09:16:03 -0500
Subject: [PATCH] Add questions/objectives to remaining episodes

---
 episodes/04_setup_project.md  | 11 +++++++++++
 episodes/05_setup_env.md      | 13 +++++++++++++
 episodes/10_reuse_workflow.md | 24 ++++++++++++++++++++----
 episodes/11_summary_rule.md   | 19 +++++++++++++------
 episodes/12_run_on_slurm.md   | 25 +++++++++++++++++++++++++
 5 files changed, 82 insertions(+), 10 deletions(-)

diff --git a/episodes/04_setup_project.md b/episodes/04_setup_project.md
index d24d277a..6274d418 100644
--- a/episodes/04_setup_project.md
+++ b/episodes/04_setup_project.md
@@ -3,6 +3,17 @@ title: "Project Setup"
 teaching: 1
 exercises: 5
 ---
+:::::::::::::::::::::::::::::::::::::: questions 
+
+- How do I create a directory with the necessary files for this class?
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+::::::::::::::::::::::::::::::::::::: objectives
+
+- Create a "SnakemakeWorkflow" directory with scripts and cached container images
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+
 
 ## Log into OSC
 - Visit https://ondemand.osc.edu/.
diff --git a/episodes/05_setup_env.md b/episodes/05_setup_env.md
index cb110c36..d3fef253 100644
--- a/episodes/05_setup_env.md
+++ b/episodes/05_setup_env.md
@@ -3,6 +3,19 @@ title: "Environment Setup"
 teaching: 1
 exercises: 4
 ---
+:::::::::::::::::::::::::::::::::::::: questions 
+
+- How do I activate the Snakemake for this class?
+- How do I start an interactive job to run snakemake on a worker node?
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+::::::::::::::::::::::::::::::::::::: objectives
+
+- Setup the shell environment
+- Verify snakemake and R versions
+- Start an interactive session on a worker node
+
+::::::::::::::::::::::::::::::::::::::::::::::::
 
 ## Software Environment Setup
 
diff --git a/episodes/10_reuse_workflow.md b/episodes/10_reuse_workflow.md
index 45384f17..0455e482 100644
--- a/episodes/10_reuse_workflow.md
+++ b/episodes/10_reuse_workflow.md
@@ -3,14 +3,28 @@ title: "Reuse another workflow"
 teaching: 10
 exercises: 2
 ---
+:::::::::::::::::::::::::::::::::::::: questions 
 
+- What do I need to do to re-use another Snakemake workflow?
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+::::::::::::::::::::::::::::::::::::: objectives
+
+- Add a module to our Snakefile to re-use parts of the BGNN_Core_Workflow workflow
+- Make changes so our workflow will be filename compatible
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+
+## Reusing Another Workflow
 To re-use a workflow you generally need:
 
-- where to find workflow - github "hdr-bgnn/BGNN_Core_Workflow"
-- what is the relative path to the Snakefile "workflow/Snakefile"
-- what tag or version to use "1.0.0"
-- what file naming convention is the workflow using
+- Where to find workflow? - github "hdr-bgnn/BGNN_Core_Workflow"
+- What is the relative path to the Snakefile? "workflow/Snakefile"
+- What tag or version to use? "1.0.0"
+- What file naming convention is the workflow using?
+- What dependencies must be manually installed?
 
+See source code for the workflow
 https://github.com/hdr-bgnn/BGNN_Core_Workflow/blob/main/workflow/Snakefile#L19
 
 ```
@@ -70,3 +84,5 @@ use rule segment_image from bgnn_core
 ```bash
 snakemake -c1 --use-singularity Segmented/bj373514_segmented.png 
 ```
+
+
diff --git a/episodes/11_summary_rule.md b/episodes/11_summary_rule.md
index f1aecd09..aea64428 100644
--- a/episodes/11_summary_rule.md
+++ b/episodes/11_summary_rule.md
@@ -4,6 +4,19 @@ teaching: 10
 exercises: 2
 ---
 
+:::::::::::::::::::::::::::::::::::::: questions 
+
+- How can we specify a rule that has many dynamic input files?
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+::::::::::::::::::::::::::::::::::::: objectives
+
+- Add a summary rule that requires Segmented images
+- Use expand function to simplify creating filenames
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+
+
 Add summary_report to config.yaml:
 ```bash
 cat Scripts/SummaryReport.R 
@@ -43,10 +56,4 @@ rule summary:
 ```
 
 
-Where did my logs go?
-```bash
-ls logs
-ls logs/
-```
-
 
diff --git a/episodes/12_run_on_slurm.md b/episodes/12_run_on_slurm.md
index 4a87122e..6c4310c8 100644
--- a/episodes/12_run_on_slurm.md
+++ b/episodes/12_run_on_slurm.md
@@ -4,6 +4,22 @@ teaching: 10
 exercises: 2
 ---
 
+:::::::::::::::::::::::::::::::::::::: questions 
+
+- How can can I add memory, cpu, and gpu requirements to a rule?
+- How can can I scale up my workflow in a cluster?
+- What logs are created when running my workflow with a cluster?
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+::::::::::::::::::::::::::::::::::::: objectives
+
+- Add a memory requirement to a rule
+- Create sbatch script to run a workflow at scale
+- Delete all outputs
+- Run the workflow at scale
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+
 ## Problems with way we have been running snakemake
 - Only using a single node so limited scaling
 - Must keep our terminal window connected or the job might stop
@@ -53,6 +69,15 @@ Run snakemake in the background scaling up
 sbatch run-workflow.sh -c10
 ```
 
+## Monitor job
 ```
 squeue -u $LOGNAME
 ```
+
+## Notice new job logs
+
+Where did my logs go?
+```bash
+ls logs
+ls logs/
+```