updated readme

naturalis · Jan 17, 2023 · 5fa3661 · 5fa3661
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diff --git a/README.md b/README.md
@@ -22,7 +22,7 @@ subsections are here:
 - [Documentation](doc), about packages and tools needed for everything in the repository.
 - [Cow_metadata_pipeline](cow_metadata_pipeline), containing the files for the pipeline, including the scripts, test data and documentation 
 - [Database](database), containing the scripts needed for transforming the data to the correct format, database schema, testdata and documentation.
-- [Variant_calling_pipeline](variant_calling_pipeline)containing the files for the variant calling pipeline, including the scripts, test data and documentation 
+- [Variant_calling_pipeline](variant_calling_pipeline), containing the files for the variant calling pipeline, including the scripts, test data and documentation 
 
 reserved zenodo doi:
 

diff --git a/cow_metadata_pipeline/README.md b/cow_metadata_pipeline/README.md
@@ -19,15 +19,15 @@ Limousin|SAMN09379797|SRS3434715|ftp.sra.ebi.ac.uk/vol1/ERZ173/ERZ1738264/ChrMT-
 
 To run the pipeline the following command can be used, after changing the yaml file to match your correct input, intermediar, and output folders, to check whether everything is setup correctly.
 
-'''
-snakemake -n -s {name of the snakefile}
-''' 
+
+	snakemake -n -s {name of the snakefile}
+
 
 If that doens't throw an error, you can run the pipeline as shown below.
 
-'''
-snakemake -c 1 -s {name of the snakefile}
-''' 
+
+	snakemake -c 1 -s {name of the snakefile}
+
 
 The yaml file is specified at the top of the snakefile and contains the following keys:
 

diff --git a/cow_metadata_pipeline/Snakefile_test → ...data_pipeline/Snakefile_metadata_pipeline b/cow_metadata_pipeline/Snakefile_test → ...data_pipeline/Snakefile_metadata_pipeline