Enable slurm-cluster-status by default

.gitmodules

+[submodule "bin/slurm-cluster-status"]
+	path = bin/slurm-cluster-status
+	url = https://github.com/LUMC/slurm-cluster-status

README.md

@@ -64,7 +64,21 @@ conda activate snakemake
 
 (This workflow has been tested with snakemake version 5.10.0
 and likely also works with newer versions.)
- 
+
+Download the workflow to your current directory with:
+
+```bash
+git clone --recurse-submodules https://git.lumc.nl/snooij/metagenomics-scaffold-classification.git
+```
+
+Optionally rename the directory to which the workflow was downloaded,
+and change into it to start using.
+
+```bash
+mv metagenomics-scaffold-classification my_awesome_classification_project
+cd my_awesome_classification_project
+```
+
 Furthermore, the workflow requires the NCBI BLAST nr database with
 its associated taxonomic information and an index for use with DIAMOND.
 These have been kindly provided by the creators of CAT and can be found
@@ -141,7 +155,7 @@ In particular the bottom two lines are essential for working with SLURM:
 
 ```yaml
 cluster: "sbatch --parsable -N 1 -n 1 -c {threads} --mem={resources.mem} -t {resources.time} -D . -e log/SLURM/{name}-{jobid}.err -o log/SLURM/{name}-{jobid}.out"
-#cluster-status: "bin/slurm-cluster-status/slurm-cluster-status.py"
+cluster-status: "bin/slurm-cluster-status/slurm-cluster-status.py"
 ```
 
 It is recommended to add `--mail-type=FAIL --mail-user=[YOUR EMAIL ADDRESS]`,
@@ -153,16 +167,9 @@ for instance.
 [`config/parameters.yaml`](config/parameters.yaml) file.
 Change these when necessary on your system.)
 
-To use the (optional) custom Python script 'slurm-cluster-status'
-that can help Snakemake communicate with SLURM, remove the comment
-sign (#) from the bottom line in `config/parameters.yaml` and
-download the script by running:
-
-```bash
-cd bin
-git clone https://github.com/LUMC/slurm-cluster-status.git
-cd ..
-```
+The (optional) custom Python script 'slurm-cluster-status'
+that can help Snakemake communicate with SLURM is used by default.
+Remove the (bottom) line in `config/parameters.yaml` to disable it.
 
 Now everything should be set to run the workflow!
 

slurm-cluster-status @ 81a18016

+Subproject commit 81a18016a4413e64a833343788fd7219448f8307

config/config.yaml

@@ -6,4 +6,4 @@ keep-going: true
 printshellcmds: true
 use-conda: true
 cluster: "sbatch --parsable -N 1 -n 1 -c {threads} --mem={resources.mem} -t {resources.time} -D . -e log/SLURM/{name}-{jobid}.err -o log/SLURM/{name}-{jobid}.out"
-#cluster-status: "bin/slurm-cluster-status/slurm-cluster-status.py"
+cluster-status: "bin/slurm-cluster-status/slurm-cluster-status.py"