From 0fef1343232fbd84bbe11f12397b454f3355ed74 Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Tue, 22 Jan 2019 11:28:34 +0100
Subject: [PATCH] Small change in Snakefile. Change in config.yaml to include
more files.
---
snakemake/process_data/Snakefile | 2 +-
snakemake/process_data/config.yaml | 10 +++++-----
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/snakemake/process_data/Snakefile b/snakemake/process_data/Snakefile
index 0d869f4..5e714a1 100644
--- a/snakemake/process_data/Snakefile
+++ b/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")
diff --git a/snakemake/process_data/config.yaml b/snakemake/process_data/config.yaml
index f3b40e9..25adcf2 100644
--- a/snakemake/process_data/config.yaml
+++ b/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}
...
--
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