From 8a43e8155675611e9fef6b39c20cbc3337af3684 Mon Sep 17 00:00:00 2001
From: samnooij <s.nooij@lumc.nl>
Date: Tue, 17 May 2022 15:47:54 +0200
Subject: [PATCH] Adapt to assembled fasta
---
README.md | 2 +-
bin/generate_sample_yaml.sh | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index aaa008c..de8e48f 100644
--- a/README.md
+++ b/README.md
@@ -122,7 +122,7 @@ done
**names in the parameters.yaml file.**
These scripts assume that:
1. Your data files are stored in `data/raw/`
-2. Your data files have names like {sample}-trimmed_R1.fastq.gz
+2. Your data files have names like `{sample}.fasta`
If those are both true for your data, use:
diff --git a/bin/generate_sample_yaml.sh b/bin/generate_sample_yaml.sh
index a86097b..003aa0e 100644
--- a/bin/generate_sample_yaml.sh
+++ b/bin/generate_sample_yaml.sh
@@ -3,8 +3,8 @@
# Generate a yaml file for the samples in data/raw
echo "samples:" > config/samples.yaml
-for sample in data/raw/*_R1.fastq.gz
+for sample in data/raw/*.fasta
do
- name="$(basename -s "-trimmed_R1.fastq.gz" $sample)"
+ name="$(basename -s ".fasta" $sample)"
printf " - ${name}\n"
done >> config/samples.yaml
--
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