added all examples for the tutorial, reworked the presentation

00-start/Snakefile

@@ -4,7 +4,7 @@ rule summarize:
 	output:
 		#TODO
 	shell:
-		"wc -c #TODO"
+		"wc -c {input} > {output}"
 
 rule extract:
 	input:
@@ -12,5 +12,4 @@ rule extract:
 	output:
 		#TODO
 	shell:
-		"cut -f7 -d ' ' #TODO"
-
+		"sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"

01-example/Snakefile

-
-
 rule all:
 	input:
 		"extract.txt"
@@ -19,8 +17,8 @@ rule extract:
 	output:
 		"extract.txt"
 	shell:
-		"cut -f7 -d ' ' {input} > {output}"
+		"sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
 
 rule clean:
 	shell:
-		"rm extract.txt sum.txt"
+		"rm -f extract.txt sum.txt"

02-expand/A.fasta

+>A
+ACATATAGAGATATAT

02-expand/B.fasta

+>B
+ACACAATCTATCATCTACTACGACGAGCGACGAGCGACGGACGAGGGTATCTATCTAGCAGC

02-expand/Snakefile

+SAMPLES = "A B".split()
+
+rule all:
+	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}"
+
+rule extract:
+	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"

03-dynamic/A.fasta

+>A
+ACATATAGAGATATAT

03-dynamic/B.fasta

+>B
+ACACAATCTATCATCTACTACGACGAGCGACGAGCGACGGACGAGGGTATCTATCTAGCAGC

03-dynamic/C.fasta

+>C
+ACAGCGAGCAGCGGCGACGAGCGACGGACGATCTATCATCTACTACGACGAGCGACGAGCGACGGACGAGGGTATCTATCTAGCAGC

03-dynamic/Snakefile

+
+SAMPLES, = glob_wildcards("{samples}.fasta")
+
+rule all:
+	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}"
+
+rule extract:
+	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"

03-dynamic/extract.txt

+20
+66
+91
+177

04-cluster/A.fasta

+>A
+ACATATAGAGATATAT

04-cluster/B.fasta

+>B
+ACACAATCTATCATCTACTACGACGAGCGACGAGCGACGGACGAGGGTATCTATCTAGCAGC

04-cluster/C.fasta

+>C
+ACAGCGAGCAGCGGCGACGAGCGACGGACGATCTATCATCTACTACGACGAGCGACGAGCGACGGACGAGGGTATCTATCTAGCAGC

04-cluster/Snakefile

+localrules: all, extract
+
+SAMPLES, = glob_wildcards("{samples}.fasta")
+
+rule all:
+	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}"
+
+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}"
+
+rule clean:
+	shell:
+		"rm -f extract.txt sum.txt"

04-cluster/sum.txt

+ 20 A.fasta
+ 66 B.fasta
+ 91 C.fasta
+177 total

05-foreach/A.fasta

+>A
+ACATATAGAGATATAT

05-foreach/B.fasta

+>B
+ACACAATCTATCATCTACTACGACGAGCGACGAGCGACGGACGAGGGTATCTATCTAGCAGC

05-foreach/C.fasta

+>C
+ACAGCGAGCAGCGGCGACGAGCGACGGACGATCTATCATCTACTACGACGAGCGACGAGCGACGGACGAGGGTATCTATCTAGCAGC

05-foreach/Snakefile

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

06-foreach-complete/A.fasta

+>A
+ACATATAGAGATATAT

06-foreach-complete/B.fasta

+>B
+ACACAATCTATCATCTACTACGACGAGCGACGAGCGACGGACGAGGGTATCTATCTAGCAGC

06-foreach-complete/C.fasta

+>C
+ACAGCGAGCAGCGGCGACGAGCGACGGACGATCTATCATCTACTACGACGAGCGACGAGCGACGGACGAGGGTATCTATCTAGCAGC

06-foreach-complete/Snakefile

+localrules: all, extract
+
+SAMPLES, = glob_wildcards("{samples}.fasta")
+
+rule all:
+	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}"
+
+rule clean:
+	shell:
+		"rm -f *.sum"

02-report/Snakefile → 07-report/Snakefile

@@ -19,11 +19,11 @@ rule extract:
 	output:
 		"extract.txt"
 	shell:
-		"cut -f7 -d ' ' {input} > {output}"
+		"sed 's/^[ ]*//' {input} | cut -f1 -d ' ' > {output}"
 
 rule clean:
 	shell:
-		"rm extract.txt sum.txt"
+		"rm -f extract.txt sum.txt"
 
 
 rule report:
@@ -38,4 +38,4 @@ rule report:
 	========
 	
 	Something  {input.T1}
-	""", output.html, metadata="Thomas Schwarzl", **input)
+	""", output.html, metadata="Author", **input)