Small change in Snakefile. Change in config.yaml to include more files.

snakemake/process_data/Snakefile

@@ -27,7 +27,7 @@ rule clip_reads:
 		v = "-v",
 		n = "-n",
 		l = "20",
-		adapter = "GATCGGAAGAGCACA", #lambda wildcards: config[wildcards.sample]['adapter'],
+		adapter = lambda wildcards: config[wildcards.sample]['adapter'],
 		z = "-z"
 	log:
 		os.path.join(config["local_log"], "clip_reads_{sample}.log")

snakemake/process_data/config.yaml

@@ -18,9 +18,9 @@
   ##############################################################################
   input_dir: "samples"
   input_reads_pattern: ".fastq.gz"
-  sample: ["example"] #, "example2", "SRR1536304", "SRR1536305"]
-  example: {adapter: "GATCGGAAGAGCACA", minimum_quality: 20, quality_type: 33}
-#  example2: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 64}
-#  SRR1536304: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}
-#  SRR1536305: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}
+  sample: ["example", "example2", "SRR1536304", "SRR1536305"]
+  example: {adapter: GATCGGAAGAGCACA, minimum_quality: 20, quality_type: 33}
+  example2: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 64}
+  SRR1536304: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}
+  SRR1536305: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}
 ...