Verified Commit 5f7e35b9 authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

add expected results

parent 283eb4b9
......@@ -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:
(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
mkdir -p ${SCRATCH}/tmp
2. Run command
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
snakemake --report
## Expected outputs
With real yeast data:
- the `snakemake` report: `report.html`, download a [copy here](
- the `multiqc` report: `results/qc/multiqc/multiqc_report.html`, download a [copy here](
# Credits
This template is derived from the official [Snakemake-workflow]( by [Antonie Vietor]( and [David Laehnemann](
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