add expected results

README.md

@@ -147,6 +147,21 @@ the command once on a `node` is:
 
 Of note, the 2 above steps can be replaced by the alias `smk` if you added the alias in your `.bashrc`
 
+It should look like this from accessing the access machine to getting the resources and activating the environment:
+
+```bash
+(base) aginolhac@access1.iris-cluster.uni.lux(14:05:02)-> 20:56): ~ $ si -c 6 -t 1:00:00
+# salloc -p interactive --qos debug -C batch 
+salloc: Pending job allocation 2424900
+salloc: job 2424900 queued and waiting for resources
+salloc: job 2424900 has been allocated resources
+salloc: Granted job allocation 2424900
+salloc: Waiting for resource configuration
+salloc: Nodes iris-139 are ready for job
+(base) aginolhac@iris-139(14:17:21)-> 29:51)(2424900 1N/T/1CN): ~ $ smk
+(snakemake) aginolhac@iris-139(14:17:23)-> 29:49)(2424900 1N/T/1CN): ~ $
+```
+
 ### Dry-run
 
 
@@ -163,7 +178,7 @@ Workflow defines that rule genome_faidx is eligible for caching between workflow
 Workflow defines that rule bwa_index is eligible for caching between workflows (use the --cache argument to enable this).
 ```
 
-are warning you that 
+are warning you that the **cache** option is not activated. This is useful is your use 
 
 
 ### Activate the cache 
@@ -172,19 +187,35 @@ To save download and computation times in between workflows
 
 1. Set-up
 
-```
+```bash
 mkdir -p ${SCRATCH}/tmp
 export SNAKEMAKE_OUTPUT_CACHE=${SCRATCH}/tmp
 ```
 
 2. Run command
 
-```
+```bash
 snakemake --use-singularity --singularity-args "-B /scratch/users/aginolhac:/scratch/users/aginolhac"  --cache -j 6
 ```
 
 
 
+3. If the previous step was successful, one can obtain the report by running
+
+```bash
+snakemake --report
+```
+
+
+## Expected outputs
+
+With real yeast data:
+
+- the `snakemake` report: `report.html`, download a [copy here](https://xsOdPxjHMEpp3hc:123456@owncloud.lcsb.uni.lu/public.php/webdav/report.html)
+- the `multiqc` report: `results/qc/multiqc/multiqc_report.html`, download a [copy here](https://xsOdPxjHMEpp3hc:123456@owncloud.lcsb.uni.lu/public.php/webdav/multiqc.html)
+
+
+
 # Credits
 
 This template is derived from the official [Snakemake-workflow](https://github.com/snakemake-workflows/chipseq) by [Antonie Vietor](https://github.com/AntonieV) and [David Laehnemann](https://github.com/dlaehnemann).