fix indentation and tabs-to-whitespace;

00-start/Snakefile

 rule summarize:
-	input:
-		#TODO
-	output:
-		#TODO
-	shell:
-		"wc -c {input} > {output}"
+    input:
+        #TODO
+    output:
+        #TODO
+    shell:
+        "wc -c {input} > {output}"
 
 rule extract:
-	input:
-		#TODO
-	output:
-		#TODO
-	shell:
-		"sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
+    input:
+        #TODO
+    output:
+        #TODO
+    shell:
+        "sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"

01-example/Snakefile

 rule all:
-	input:
-		"extract.txt"
+    input:
+        "extract.txt"
 
 rule summarize:
-	input:
-		"A.fasta",
-		"B.fasta"
-	output:
-		"sum.txt"
-	shell:
-		"wc -c {input} > {output}"
+    input:
+        "A.fasta",
+        "B.fasta"
+    output:
+        "sum.txt"
+    shell:
+        "wc -c {input} > {output}"
 
 rule extract:
-	input:
-		"sum.txt"
-	output:
-		"extract.txt"
-	shell:
-		"sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
+    input:
+        "sum.txt"
+    output:
+        "extract.txt"
+    shell:
+        "sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
 
 rule clean:
-	shell:
-		"rm -f extract.txt sum.txt"
+    shell:
+        "rm -f extract.txt sum.txt"

02-expand/Snakefile

 SAMPLES = "A B".split()
 
 rule all:
-	input:
-		"extract.txt"
+    input:
+        "extract.txt"
 
 rule summarize:
-	input:
-		expand("{samples}.fasta", samples=SAMPLES)
-	output:
-		"sum.txt"
-  message:
-    "summarizing counts from {input} and creating {output}"
-	shell:
-		"wc -c {input} > {output}"
+    input:
+        expand("{samples}.fasta", samples=SAMPLES)
+    output:
+        "sum.txt"
+    message:
+        "summarizing counts from {input} and creating {output}"
+    shell:
+        "wc -c {input} > {output}"
 
 rule extract:
-	input:
-		"sum.txt"
-	output:
-		"extract.txt"
-  message:
-    "extracting the counts"
-	shell:
-		"sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
+    input:
+        "sum.txt"
+    output:
+        "extract.txt"
+    message:
+        "extracting the counts"
+    shell:
+        "sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
 
 rule clean:
-	shell:
-		"rm -f extract.txt sum.txt"
+    shell:
+        "rm -f extract.txt sum.txt"

03-dynamic/Snakefile

@@ -2,29 +2,29 @@
 SAMPLES, = glob_wildcards("{samples}.fasta")
 
 rule all:
-	input:
-		"extract.txt"
+    input:
+        "extract.txt"
 
 rule summarize:
-	input:
-		expand("{samples}.fasta", samples=SAMPLES)
-	output:
-		temp("sum.txt")
-	message:
-		"summarizing counts from {input} and creating {output}"
-	shell:
-		"wc -c {input} > {output}"
+    input:
+        expand("{samples}.fasta", samples=SAMPLES)
+    output:
+        temp("sum.txt")
+    message:
+        "summarizing counts from {input} and creating {output}"
+    shell:
+        "wc -c {input} > {output}"
 
 rule extract:
-	input:
-		"sum.txt"
-	output:
-		"extract.txt"
-	message:
-		"extracting the counts"
-	shell:
-		"sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
+    input:
+        "sum.txt"
+    output:
+        "extract.txt"
+    message:
+        "extracting the counts"
+    shell:
+        "sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
 
 rule clean:
-	shell:
-		"rm -f extract.txt sum.txt"
+    shell:
+        "rm -f extract.txt sum.txt"

04-cluster/Snakefile

@@ -3,33 +3,33 @@ localrules: all, extract
 SAMPLES, = glob_wildcards("{samples}.fasta")
 
 rule all:
-	input:
-		"extract.txt"
+    input:
+        "extract.txt"
 
 rule summarize:
-	input:
-		expand("{samples}.fasta", samples=SAMPLES)
-	output:
-		temp("sum.txt")
-	message:
-		"summarizing counts from {input} and creating {output}"
-	log:
-		"sum.log"
-	shell:
-		"wc -c {input} > {output} 2> {log}"
+    input:
+        expand("{samples}.fasta", samples=SAMPLES)
+    output:
+        temp("sum.txt")
+    message:
+        "summarizing counts from {input} and creating {output}"
+    log:
+        "sum.log"
+    shell:
+        "wc -c {input} > {output} 2> {log}"
 
 rule extract:
-	input:
-		"sum.txt"
-	output:
-		"extract.txt"
-	message:
-		"extracting the counts"
-	log:
-		"sum.log"
-	shell:
-		"sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output} 2> {log}"
+    input:
+        "sum.txt"
+    output:
+        "extract.txt"
+    message:
+        "extracting the counts"
+    log:
+        "sum.log"
+    shell:
+        "sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output} 2> {log}"
 
 rule clean:
-	shell:
-		"rm -f extract.txt sum.txt"
+    shell:
+        "rm -f extract.txt sum.txt"

05-foreach/Snakefile

@@ -3,19 +3,19 @@ localrules: all, extract
 SAMPLES, = glob_wildcards("{samples}.fasta")
 
 rule all:
-	input:
-		#TODO
+    input:
+        #TODO
 
 rule do_summarize:
-	input:
-		#TODO
-	output:
-		#TODO
-	message:
-		"summarizing {input} to {output}"
-	shell:
-		"wc -c {input} > {output}"
+    input:
+        #TODO
+    output:
+        #TODO
+    message:
+        "summarizing {input} to {output}"
+    shell:
+        "wc -c {input} > {output}"
 
 rule clean:
-	shell:
-		"rm -f *.sum"
+    shell:
+        "rm -f *.sum"

06-foreach-complete/Snakefile

@@ -3,19 +3,19 @@ localrules: all, extract
 SAMPLES, = glob_wildcards("{samples}.fasta")
 
 rule all:
-	input:
-		expand("{samples}.sum", samples=SAMPLES)
+    input:
+        expand("{samples}.sum", samples=SAMPLES)
 
 rule do_summarize:
-	input:
-		"{samples}.fasta"
-	output:
-		"{samples}.sum"
-	message:
-		"summarizing {input} to {output}"
-	shell:
-		"wc -c {input} > {output}"
+    input:
+        "{samples}.fasta"
+    output:
+        "{samples}.sum"
+    message:
+        "summarizing {input} to {output}"
+    shell:
+        "wc -c {input} > {output}"
 
 rule clean:
-	shell:
-		"rm -f *.sum"
+    shell:
+        "rm -f *.sum"

07-report/Snakefile

 from snakemake.utils import report
 
 rule all:
-	input:
-		"extract.txt"
+    input:
+        "extract.txt"
 
 rule summarize:
-	input:
-		"A.fasta",
-		"B.fasta"
-	output:
-		"sum.txt"
-	shell:
-		"wc -c {input} > {output}"
+    input:
+        "A.fasta",
+        "B.fasta"
+    output:
+        "sum.txt"
+    shell:
+        "wc -c {input} > {output}"
 
 rule extract:
-	input:
-		"sum.txt"
-	output:
-		"extract.txt"
-	shell:
-		"sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
+    input:
+        "sum.txt"
+    output:
+        "extract.txt"
+    shell:
+        "sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
 
 rule clean:
-	shell:
-		"rm -f extract.txt sum.txt"
+    shell:
+        "rm -f extract.txt sum.txt"
 
 
 rule report:
-	input:
-		T1="sum.txt"
-	output:
-		html="report.html"
-	run:
-		report("""
-	========
-	title
-	========
-	
-	Something  {input.T1}
-	""", output.html, metadata="Author", **input)
+    input:
+        T1="sum.txt"
+    output:
+        html="report.html"
+    run:
+        report("""
+    ========
+    title
+    ========
+
+    Something  {input.T1}
+    """, output.html, metadata="Author", **input)

README.md

@@ -3,13 +3,14 @@
 Presentation and Example files
 
 
-## Start the tutorial 
+## Start the tutorial
 
 The folder 00-start contains all files for starting the tutorial.
 
-A.fasta - input file
-B.fasta - input file
-Snakefile - skeleton Snakefile
+- Inputs:
+    - A.fasta
+    - B.fasta
+- Snakefile (skeleton)
 
 
 ## First example
@@ -20,7 +21,3 @@ The folder 01-example contains the first simple example
 ## Report
 
 The folder 02-report contains an example for creating a html report
-
-
-
-