Merge pull request #1080 from nextstrain/remove-augur-recursion-limit

Remove AUGUR_RECURSION_LIMIT

Snakefile

@@ -12,10 +12,6 @@ from collections import OrderedDict
 import textwrap
 import time
 
-# Set the maximum recursion limit globally for all shell commands, to avoid
-# issues with large trees crashing the workflow.  Preserve Snakemake's default
-# use of Bash's "strict mode", as we rely on that behaviour.
-shell.prefix("set -euo pipefail; export AUGUR_RECURSION_LIMIT=10000; ")
 
 # Store the user's configuration prior to loading defaults, so we can check for
 # reused subsampling scheme names in the user's config. We need to make a deep

nextstrain_profiles/nextstrain-scicore/submit.sh

@@ -1,14 +1,11 @@
 #!/bin/sh
- 
+
 #SBATCH --output=log/%j.out                 # where to store the output ( %j is the JOBID )
 #SBATCH --error=log/%j.err                  # where to store error messages
 
 # activate conda environment
 source /scicore/home/neher/neher/miniconda3/etc/profile.d/conda.sh
 conda activate nextstrain
 export AUGUR_MINIFY_JSON=1
-export AUGUR_RECURSION_LIMIT=10000
 
 {exec_job}
-
-