Update README.md

README.md

@@ -5,6 +5,7 @@
 * wget
 * git
 * singularity
+* Slurm Workload Manager
 
 ## Features
 
@@ -85,10 +86,42 @@ gunzip Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
 
 Then download rRNAs (e.g. from RefSeq). For the members of the group you can use the following file:
 ```
-cp /scicore/home/zavolan/gypas/projects/resources/human/rRNA/rRNA_joao.fa
+cp /scicore/home/zavolan/gypas/projects/resources/human/rRNA/txome_rRNAs_joao.fa .
 ```
 
 Finally copy or create a file with oligos. For the members of the group you can use the following file:
 ```
-cp /scicore/home/zavolan/gypas/projects/resources/human/rRNA/oligos.txt
-```
\ No newline at end of file
+cp /scicore/home/zavolan/gypas/projects/resources/human/rRNA/oligos.txt .
+```
+
+### Configure and run workflows
+
+As mentioned earlier two snakemake workflows are available. One that prepares the annotation files (e.g. generation of index files etc) and one that processes the Ribo-Seq data.
+
+#### Prepare annotation workflow
+
+First of all go to the 'snakemake/prepare_annotation' directory and fill in the 'config.yaml' file. To make sure that everything is configured properly create a dag of the workflow.
+
+```
+bash create_snakemake_flowchart.sh
+```
+
+And finally run the pipeline. This script is configured for the Slurm Workload Manager
+```
+nohup bash run_snakefile.sh &
+```
+#### Process data workflow
+
+Once the prepare_annotation pipeline is complete you can move to the 'snakemake/process_data' directory. Copy or create a hard link of the Ribo-Seq samples you want to process in the 'samples' directory. Fill in the config.yaml file. 
+
+Create the dag
+```
+bash create_snakemake_flowchart.sh
+```
+
+And finally run the pipeline. This script is configured for the Slurm Workload Manager
+```
+nohup bash run_snakefile.sh &
+```
+
+