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: ...@@ -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` 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 ### Dry-run
...@@ -163,7 +178,7 @@ Workflow defines that rule genome_faidx is eligible for caching between workflow ...@@ -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). 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 ### Activate the cache
...@@ -172,19 +187,35 @@ To save download and computation times in between workflows ...@@ -172,19 +187,35 @@ To save download and computation times in between workflows
1. Set-up 1. Set-up
``` ```bash
mkdir -p ${SCRATCH}/tmp mkdir -p ${SCRATCH}/tmp
export SNAKEMAKE_OUTPUT_CACHE=${SCRATCH}/tmp export SNAKEMAKE_OUTPUT_CACHE=${SCRATCH}/tmp
``` ```
2. Run command 2. Run command
``` ```bash
snakemake --use-singularity --singularity-args "-B /scratch/users/aginolhac:/scratch/users/aginolhac" --cache -j 6 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 # 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). 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).
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