diff --git a/Snakemake/IMAGE_calling/README.md b/Snakemake/IMAGE_calling/README.md
index 9d1598fa2cbf88b051c70976cf1b00b7a5a4eea3..c5b1dea01ac19a967ed2320614856b1b04b31ddf 100644
--- a/Snakemake/IMAGE_calling/README.md
+++ b/Snakemake/IMAGE_calling/README.md
@@ -180,7 +180,7 @@ Absolut paths need to be precise in the config.yaml
# Configure workflow and running workflow
- Copy the config.yaml file into your working directory and update it according to the instructions inside the file.
-- If necessary update resources_SLURM.yaml to define cpu and memory resources for each rule. The default section is the minimal resources per job. The other section take as name the rules name and define only resources that are different from the default section.
+- If necessary update resources_SLURM.yaml to define cpu, memory and cluster partition resources for each rule. The default section is the minimal resources per job. The other section take as name the rules name and define only resources that are different from the default section.
- launch snakemake command as presented in SLURM.sh to launch the workflow.
Resources_SLURM.yaml and SLURM.sh are specific to SLURM cluster. Therefore, if you use another cluster, you need to create other files. However, you can use these files to inspire you.
diff --git a/Snakemake/IMAGE_calling/SLURM.sh b/Snakemake/IMAGE_calling/SLURM.sh
index 200ffaf0dcbf2101b975221ed35657cb4701a6d6..0fbffe4e0bae9ace7e38cd42acb7d02b45910fa2 100755
--- a/Snakemake/IMAGE_calling/SLURM.sh
+++ b/Snakemake/IMAGE_calling/SLURM.sh
@@ -17,8 +17,8 @@ snakemake -s $WORKFLOW_DIR/Snakefile --printshellcmds --jobs 200 \
--configfile config.yaml --dryrun
# This is an example of the snakemake command line to launch on a SLURM cluster
- # {cluster.cpu} and {cluster.mem} will be replace by value defined in the resources_SLURM.yaml file
+ # {cluster.cpu}, {cluster.mem} and {cluster.partition} will be replace by value defined in the resources_SLURM.yaml file
snakemake -s $WORKFLOW_DIR/Snakefile --printshellcmds --jobs 200 \
--configfile config.yaml \
--cluster-config $WORKFLOW_DIR/resources_SLURM.yaml \
- --cluster "sbatch --cpus-per-task={cluster.cpu} --mem-per-cpu={cluster.mem} --error=logs/%x.stderr --output=logs/%x.stdout " --latency-wait 30
+ --cluster "sbatch -p {cluster.partition} --cpus-per-task={cluster.cpu} --mem-per-cpu={cluster.mem} --error=logs/%x.stderr --output=logs/%x.stdout " --latency-wait 30
diff --git a/Snakemake/IMAGE_calling/resources_SLURM.yaml b/Snakemake/IMAGE_calling/resources_SLURM.yaml
index 4c279c61dd25c61ccb547175a190cbd21973beb9..1bf89ab7af81d29d06c2b5eb5735a434b0cff112 100644
--- a/Snakemake/IMAGE_calling/resources_SLURM.yaml
+++ b/Snakemake/IMAGE_calling/resources_SLURM.yaml
@@ -1,6 +1,7 @@
__default__ :
mem : "7G"
cpu : 1
+ partition : "workq"
fastqc :
cpu : 8
@@ -38,12 +39,15 @@ AnalyzeCovariates:
HaplotypeCaller :
mem : "30G"
+ partition : "unlimitq"
CombineGVCFs :
mem : "60G"
+ partition : "unlimitq"
GenotypeGVCFs :
mem : "60G"
+ partition : "unlimitq"
freebayes:
mem : "30G"
diff --git a/Snakemake/IMAGE_vqsr/README.md b/Snakemake/IMAGE_vqsr/README.md
index 52c36e75580a4e3bcef436ff5d7e499856f10648..f06c00af004f25c90a997699091f1b87e6c977d7 100644
--- a/Snakemake/IMAGE_vqsr/README.md
+++ b/Snakemake/IMAGE_vqsr/README.md
@@ -140,7 +140,7 @@ For the final step, the python script filter_multi_sample_vcf.py need PyVCF for
## 4. Configure and running workflow
- Copy the config.yaml file into your working directory and update it according to the instructions inside the file.
-- If necessary update resources_SLURM.yaml to define cpu and memory resources for each rule. The default section is the minimal resources per job. The other section take as name the rules name and define only resources that are different from the default section.
+- If necessary update resources_SLURM.yaml to define cpu memory and cluster partition resources for each rule. The default section is the minimal resources per job. The other section take as name the rules name and define only resources that are different from the default section.
- launch snakemake command as presented in SLURM.sh to launch the workflow.
Resources_SLURM.yaml and SLURM.sh are specific to SLURM cluster. Therefore, if you use another cluster, you need to create other files. However, you can use these files to inspire you.
diff --git a/Snakemake/IMAGE_vqsr/SLURM.sh b/Snakemake/IMAGE_vqsr/SLURM.sh
new file mode 100644
index 0000000000000000000000000000000000000000..91ce33425ad209462bf7603f08bfb081fe7a2db4
--- /dev/null
+++ b/Snakemake/IMAGE_vqsr/SLURM.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+##############################################################################
+## launch workflow
+
+# if used on Genologin cluster (INRA Toulouse )
+# module load system/Python-3.6.3
+# and because we are not using module for all other dependencies, you need to add vcftool librairy in the PERL5LIB environment variable
+# export PERL5LIB=/usr/local/bioinfo/src/VCFtools/vcftools-0.1.15/src/perl/:$PERL5LIB
+
+WORKFLOW_DIR=??
+
+mkdir -p logs
+
+# This is an example of the snakemake command line to launch a dryrun
+snakemake -s $WORKFLOW_DIR/Snakefile --printshellcmds --jobs 200 \
+ --configfile config.yaml --dryrun
+
+# This is an example of the snakemake command line to launch on a SLURM cluster
+ # {cluster.cpu}, {cluster.mem} and {cluster.partition} will be replace by value defined in the resources_SLURM.yaml file
+snakemake -s $WORKFLOW_DIR/Snakefile --printshellcmds --jobs 200 \
+ --configfile config.yaml \
+ --cluster-config $WORKFLOW_DIR/resources_SLURM.yaml \
+ --cluster "sbatch -p {cluster.partition} --cpus-per-task={cluster.cpu} --mem-per-cpu={cluster.mem} --error=logs/%x.stderr --output=logs/%x.stdout " --latency-wait 30
diff --git a/Snakemake/IMAGE_vqsr/resources_SLURM.yaml b/Snakemake/IMAGE_vqsr/resources_SLURM.yaml
index 0bfc71c4aac280f0caed75dbb3b23ed293cd883c..deed11b7481a658898d653df5f28d7a9d34bc2a8 100644
--- a/Snakemake/IMAGE_vqsr/resources_SLURM.yaml
+++ b/Snakemake/IMAGE_vqsr/resources_SLURM.yaml
@@ -1,3 +1,4 @@
__default__:
mem : "20G"
cpu : 1
+ partition : "workq"
diff --git a/Snakemake/IMAGE_vqsr/test_SLURM.sh b/Snakemake/IMAGE_vqsr/test_SLURM.sh
deleted file mode 100644
index 7fd95647b8496de2f16134bab369cc93ddd6dcaf..0000000000000000000000000000000000000000
--- a/Snakemake/IMAGE_vqsr/test_SLURM.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/sh
-
-
-###############
-# module load #
-###############
-
-# if used on Genologin cluster (INRA Toulouse )
-# module load system/Python-3.6.3
-# and because we are not using module for all other dependencies, you need to add vcftool librairy in the PERL5LIB environment variable
-# export PERL5LIB=/usr/local/bioinfo/src/VCFtools/vcftools-0.1.15/src/perl/:$PERL5LIB
-
-
-###############
-# dryrun #
-###############
-
-#~ snakemake -s Snakefile -p --jobs 999 \
- #~ --configfile config.yaml \
- #~ --cluster-config resources_SLURM.yaml \
- #~ --cluster "sbatch --cpus-per-task={cluster.cpu} --mem={cluster.mem} --error=SLURM_logs/%x.stderr --output=SLURM_logs/%x.stdout " --latency-wait 30 --dryrun
-
-###############
-# run #
-###############
-
-# sbatch -J gatk_variantFiltration_SnakemakeTest_run1 -o SLURM_logs/%x.out -e SLURM_logs/%x.err test_SLURM.sh
-
-mkdir -p SLURM_logs/run1
-
-snakemake -s Snakefile -p --jobs 999 \
- --configfile config.yaml \
- --cluster-config resources_SLURM.yaml \
- --cluster "sbatch --cpus-per-task={cluster.cpu} --mem={cluster.mem} --error=SLURM_logs/run1/%x.stderr --output=SLURM_logs/ruhn1/%x.stdout " --latency-wait 30