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Commit e90cd15e authored by Manavalan Gajapathy's avatar Manavalan Gajapathy
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applies cleanenv to singularity - #28

parent a80f9225
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1 merge request!2QC under one umbrella (well mostly) under QuaC
......@@ -130,7 +130,7 @@ def create_snakemake_command(args, repo_path, mount_paths):
f"--restart-times {args.rerun_failed}",
"--use-conda",
"--use-singularity",
f"--singularity-args '--bind {tmp_dir}:/tmp --bind {mount_paths}'",
f"--singularity-args '--cleanenv --bind {tmp_dir}:/tmp --bind {mount_paths}'",
f"--profile '{snakemake_profile_dir}'",
f"--cluster-config '{args.cluster_config}'",
"--cluster 'sbatch --ntasks {cluster.ntasks} --partition {cluster.partition}"
......
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