Adapt to assembled fasta

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:
 

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