Bump snakemake version that fixes the reported time in snakemake report.

README.md

@@ -139,7 +139,7 @@ bash tests/test_integration_workflow_with_conda/test.slurm.sh
 
 > **NOTE:** Depending on the configuration of your Slurm installation or if
 > using a different workload manager, you may need to adapt file `cluster.json`
-> and the arguments to options `--config` and `--cores` in the file
+> and the arguments to options `--config`, `--cores` and `--jobs` in the file
 > `test.slurm.sh`, both located in directory `tests/test_integration_workflow`.
 > Consult the manual of your workload manager as well as the section of the
 > Snakemake manual dealing with [cluster execution].
@@ -210,6 +210,7 @@ your run.
         --cluster-config="cluster.json" \
         --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
         --cores=256 \
+        --jobs=256 \
         --printshellcmds \
         --rerun-incomplete \
         --use-singularity \

install/environment.yml

@@ -12,5 +12,4 @@ dependencies:
   - python=3.7.4
   - pip:
     - pandas==1.0.1
-    - snakemake==5.19.2
-
+    - snakemake==6.5.5
\ No newline at end of file

tests/test_integration_workflow/test.slurm.sh

@@ -31,6 +31,7 @@ snakemake \
     --cluster-config="../input_files/cluster.json" \
     --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
     --cores=256 \
+    --jobs=256 \
     --printshellcmds \
     --rerun-incomplete \
     --use-singularity \

tests/test_integration_workflow_multiple_lanes/test.slurm.sh

@@ -31,6 +31,7 @@ snakemake \
     --cluster-config="../input_files/cluster.json" \
     --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
     --cores=256 \
+    --jobs=256 \
     --printshellcmds \
     --rerun-incomplete \
     --use-singularity \

tests/test_integration_workflow_with_conda/test.slurm.sh

@@ -31,6 +31,7 @@ snakemake \
     --cluster-config="../input_files/cluster.json" \
     --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
     --cores=256 \
+    --jobs=256 \
     --printshellcmds \
     --rerun-incomplete \
     --use-conda \