From 37910a095f94d8af17ad11dfed69dd1aaa9c1a0b Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Fri, 16 Jul 2021 19:15:25 +0200
Subject: [PATCH] Bump snakemake version that fixes the reported time in
snakemake report.
---
README.md | 3 ++-
install/environment.yml | 3 +--
tests/test_integration_workflow/test.slurm.sh | 1 +
tests/test_integration_workflow_multiple_lanes/test.slurm.sh | 1 +
tests/test_integration_workflow_with_conda/test.slurm.sh | 1 +
5 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index 68a667e..8567fff 100644
--- a/README.md
+++ b/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 \
diff --git a/install/environment.yml b/install/environment.yml
index 8fcba7a..e28326d 100644
--- a/install/environment.yml
+++ b/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
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index 6c40abb..22f2f52 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/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 \
diff --git a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
index 10a2752..c16a757 100755
--- a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
+++ b/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 \
diff --git a/tests/test_integration_workflow_with_conda/test.slurm.sh b/tests/test_integration_workflow_with_conda/test.slurm.sh
index 873f17b..3fe2491 100755
--- a/tests/test_integration_workflow_with_conda/test.slurm.sh
+++ b/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 \
--
GitLab