Explain that multiple samples can be run now

README.md

@@ -7,7 +7,7 @@ Preliminary SV calling using Strand-seq data - summarized in a [Snakemake](https
 ### How to use it
 
   1. **Install required software:**
-  
+
     * Install [mosaicatcher](https://github.com/friendsofstrandseq/mosaicatcher) (*currently you will need the `develop` branch*)
     * Get the R-scripts from [strandsequtils](https://github.com/friendsofstrandseq/strandsequtils)
     * Install BSgenome.Hsapiens.UCSC.hg38:
@@ -18,15 +18,20 @@ Preliminary SV calling using Strand-seq data - summarized in a [Snakemake](https
     * [Strand-Phaser](https://github.com/daewoooo/StrandPhaseR) is installed automagically
 
   2. **Set up the configuration of the smakemake pipeline**
-  
-    * Open `Snake.config.json` and specify the path to the executatables (such as Mosaicatcher) and to the R scripts.
-    * Create a subdirectory `bam` and copy (or soft-link) the Strand-seq single-cell libraries in there. Note that bam files need to contain a read group and should have duplicates marked.
-   
+
+    * Open `Snake.config.json` and specify the path to the executatables
+      (such as Mosaicatcher) and to the R scripts.
+    * Create a subdirectory `bam/` and another subdirectory per sample (e.g.
+      `bam/NA12878`). **Multiple samples can be run together not**.
+      Then copy (or soft-link) the Strand-seq single-cell libraries (one BAM
+      file per cell) in there. Note that bam files need to contain a read group
+      and should have duplicates marked.
+
   3. **Run Snakemake**
 
     * run `snakemake` to compute all tasks locally
-    * Alternatively, you can ask Snakemake to submit your jobs to a HPC cluster. To this end edit the `Snake.cluster.json` file according to your available HPC environment and call 
-      
+    * Alternatively, you can ask Snakemake to submit your jobs to a HPC cluster. To this end edit the `Snake.cluster.json` file according to your available HPC environment and call
+
       ```
       snakemake -j 100 \
         --cluster-config Snake.cluster.json \