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Commit 0fef1343 authored by BIOPZ-Gypas Foivos's avatar BIOPZ-Gypas Foivos
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Small change in Snakefile. Change in config.yaml to include more files.

parent 211ef70e
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......@@ -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")
......
......@@ -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}
...
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