configs: sbatch.sh: run snakemake only if conda env activation has worked

config/GDB/sbatch.sh

@@ -10,15 +10,14 @@
 #SBATCH --qos=qos-batch
 
 # conda env name or path
-ONTP_ENV="ONT_pilot"
+ONTP_ENV="ONT_pilot" # CHANGE as needed
 # config files
 ONTP_CONFIG="config/GDB/config.yaml"
 ONTP_SLURM="config/GDB/slurm.yaml"
 # slurm cluster call
 ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}"
 
-conda activate ${ONTP_ENV}
-
+conda activate ${ONTP_ENV} && \
 snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \
 --configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
 --cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"

config/GIS20/sbatch.sh

@@ -10,15 +10,14 @@
 #SBATCH --qos=qos-batch
 
 # conda env name or path
-ONTP_ENV="conda activate /scratch/users/vgalata/miniconda3/ONT_pilot"
+ONTP_ENV="ONT_pilot" # CHANGE as needed
 # config files
 ONTP_CONFIG="config/GIS20/config.yaml"
 ONTP_SLURM="config/GIS20/slurm.yaml"
 # slurm cluster call
 ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}"
 
-conda activate ${ONTP_ENV}
-
+conda activate ${ONTP_ENV} && \
 snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \
 --configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
 --cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"

config/Zymo/sbatch.sh

@@ -10,15 +10,14 @@
 #SBATCH --qos=qos-batch
 
 # conda env name or path
-ONTP_ENV="conda activate /scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed
+ONTP_ENV="ONT_pilot" # CHANGE as needed
 # config files
 ONTP_CONFIG="config/Zymo/config.yaml"
 ONTP_SLURM="config/Zymo/slurm.yaml"
 # slurm cluster call
 ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}"
 
-conda activate ${ONTP_ENV}
-
+conda activate ${ONTP_ENV} && \
 snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \
 --configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
 --cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"