naming simplified ex1

Author: twsaari

img/rg-ex-1a.pdf

@@ -1,6 +1,6 @@
-# Snakemake toy example 
+# Snakemake toy example
 
-This is a simple toy example that can be used to start learning the basics of snakemake. This folder contains some data files with simple contents. For example, file 123.txt contains three lines of data, with values 1, 2, and 3. We'll use these simple data along with core command-line tools, included by default in most unix environments, to illustrate the basics of snakemake.
+This is a simple toy example that can be used to start learning the basics of snakemake. This folder contains some extremely simple input files. For example, sampleA.txt contains three lines of data, with values 1, 2, and 3, respectively. We'll use these simple data along with core command-line tools, included by default in most unix environments, to illustrate the basics of snakemake.
 
 Note: If you haven't installed snakemake yet, I'd suggest using [conda](https://docs.conda.io/en/latest/miniconda.html) to do so.
 
@@ -13,14 +13,14 @@ Get started by expanding Example 1a
 
 <details><summary>Expand - Ex. 1a</summary>
 
-Create a file named toy.snakefile with the following contents:
+ex-1a.smk has the following contents:
 
     rule all:
         input:
-            "output/123_rsorted.txt",
-            "output/345_rsorted.txt",
-            "output/567_rsorted.txt"
-            
+            "output/sampleA_rsorted.txt",
+            "output/sampleB_rsorted.txt",
+            "output/sampleC_rsorted.txt"
+
     rule rsort:
         input:
             "{basename}.txt"
@@ -29,6 +29,10 @@ Create a file named toy.snakefile with the following contents:
         shell:
             "sort -r {input} > {output}"
 
+<details><summary>Ex. 1a rulegraph</summary>
+![Ex. 1a rulegraph](../img/rg-ex-1a.pdf)
+</details>
+
 Topics covered:
 * Targets & dependencies
 * Writing rules
@@ -42,13 +46,13 @@ Writing rules - Generally will have 'input', 'output', and 'shell' blocks (more
 
 The rule 'all' is placed at the top of the file (the first rule, anyway), and this is always executed by default. It's being used to define the targets for the workflow.
 
-Now perform a dry-run:
+To perform a dry-run:
 
-    snakemake --snakefile toy.snakefile --dry-run
+    snakemake --snakefile ex-1a.smk --dry-run
 
 Notice that snakemake keeps track of the wildcards during the evaluation of each rule
 * experiment by changing the targets so they don't match the input files
-            
+
 ## You have reached the end of example 1a ✅
 
 </details>
@@ -59,7 +63,7 @@ Now we'll make the workflow a bit more interesting. We'll add more rules, use a
 <details><summary>Expand - Ex. 1b</summary>
 
 
-toy.snakefile contents:
+ex-1b.smk contents:
 
     rule all:
       input:
@@ -87,7 +91,7 @@ toy.snakefile contents:
 
     rule randsort:
       input:
-        "{base}.txt"
+        "output/{base}_appended.txt"
       output:
         "output/{base}_randsorted.txt"
       shell:
@@ -100,34 +104,38 @@ toy.snakefile contents:
         "output/{base}_fsorted.txt"
       shell:
         "sleep 2 ; sort -n {input} > {output}"
-        
-toy_config.yml contents:
+
+config-ex-1b.yml contents:
 
     basenames:
-      - '123'
-      - '345'
-      - '567'
+      - 'sampleA'
+      - 'sampleB'
+      - 'sampleC'
     append_val: 42
 
+<details><summary>Ex. 1b rulegraph</summary>
+![Ex. 1b rulegraph](../img/rg-ex-1b.pdf)
+</details>
+
 The config
 * How is the config used with this snakefile?
-        
+
 The expand statement
 * The various uses of curly braces can be confusing at first (at least for me)
 * `expand` is distinct from `wildcards`
 * can be thought of as "expand this string (arg 1) into an array of strings, filling in all combinations of values (args 2+ as key-value pairs)
 
 Running the new snakefile/configfile
 
-    snakemake --snakefile toy.snakefile --configfile toy_config.yml
-        
+    snakemake --snakefile ex-1b.smk --configfile config-ex-1b.yml
+
 Did snakemake run the workflow, and successfully create the desired targets?
 * View the directory of results
 
 More about the core tenets of snakemake (also gnu make, make-like things)
-* Try running the workflow to completion, then running it again. What happens? 
+* Try running the workflow to completion, then running it again. What happens?
 * Delete `output`, then try again. Isn't this cool?
-* Try deleting an intermediate file, then running the pipeline again. How is this beneficial? How can it be problematic?
+* Try modifying an intermediate file, then running the pipeline again. How is this beneficial? How can it be problematic?
 
 The workflow & DAG
 * Directed Acyclic Graph - how snakemake 'knows' how to produce the desired targets
@@ -136,11 +144,10 @@ The workflow & DAG
 Viewing the DAG (or rulegraph)
 
     #DAG (file-level granularity)
-    snakemake --snakefile toy.snakefile --configfile toy_config.yml --dag | dot -T pdf > toy_dag.pdf
+    snakemake --snakefile ex-1b.smk --configfile config-ex-1b.yml --dag | dot -T pdf > dag-ex-1b.pdf
     #Rulegraph (rule-level granularity)
-    snakemake --snakefile toy.snakefile --configfile toy_config.yml --rulegraph | dot -T pdf > toy_rulegraph.pdf
+    snakemake --snakefile ex-1b.smk --configfile config-ex-1b.yml --rulegraph | dot -T pdf > rg-ex-1b.pdf
 
 ## You have reached the end of example 1b ✅
 
 </details>
-

img/rg-ex-1b.pdf

@@ -0,0 +1,5 @@
+basenames:
+  - sampleA
+  - sampleB
+  - sampleC
+append_val: 42

toy_example/README.md

@@ -0,0 +1,13 @@
+rule all:
+    input:
+        "output/sampleA_rsorted.txt",
+        "output/sampleB_rsorted.txt",
+        "output/sampleC_rsorted.txt"
+        
+rule rsort:
+    input:
+        "{basename}.txt"
+    output:
+        "output/{basename}_rsorted.txt"
+    shell:
+        "sort -r {input} > {output}"

toy_example/config-ex-1b.smk

@@ -0,0 +1,40 @@
+rule all:
+  input:
+    expand("output/{bname}_fsorted.txt", bname=config['basenames']),
+    expand("output/{bname}_randsorted.txt", bname=config['basenames'])
+
+rule rsort:
+  input:
+    "{base}.txt"
+  output:
+    "output/{base}_rsorted.txt"
+  shell:
+    "sort -r {input} > {output}"
+
+rule append_value:
+  input:
+    "output/{base}_rsorted.txt"
+  output:
+    "output/{base}_appended.txt"
+  params:
+    append_val = config['append_val']
+  shell:
+    "cat {input} > {output} ; "
+    "echo {params.append_val} >> {output}"
+
+rule randsort:
+  input:
+    "output/{base}_appended.txt"
+  output:
+    "output/{base}_randsorted.txt"
+  shell:
+    "sort -R {input} > {output}"
+
+rule fsort:
+  input:
+    "output/{base}_appended.txt"
+  output:
+    "output/{base}_fsorted.txt"
+  shell:
+    "sleep 2 ; sort -n {input} > {output}"
+