set cluster-retries default to 3

binchicken/binchicken.py

@@ -1047,7 +1047,7 @@ def add_general_snakemake_options(argument_group, required_conda_prefix=False):
                                     help="Snakemake profile (see https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles).\n"
                                          "Can be used to submit rules as jobs to cluster engine (see https://snakemake.readthedocs.io/en/stable/executing/cluster.html).")
         argument_group.add_argument("--local-cores", type=int, help="Maximum number of cores to use on localrules when running in cluster mode", default=1)
-        argument_group.add_argument("--cluster-retries", help="Number of times to retry a failed job when using cluster submission (see `--snakemake-profile`).", default=0)
+        argument_group.add_argument("--cluster-retries", help="Number of times to retry a failed job when using cluster submission (see `--snakemake-profile`).", default=3)
         argument_group.add_argument("--snakemake-args", help="Additional commands to be supplied to snakemake in the form of a space-prefixed single string e.g. \" --quiet\"", default="")
         argument_group.add_argument("--tmp-dir", help="Path to temporary directory. [default: Use path from TMPDIR env variable]")
 

docs/preludes/coassemble_prelude.md

@@ -21,7 +21,7 @@ binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --si
 # Create snakemake profile at ~/.config/snakemake/qsub with cluster, cluster-status, cluster-cancel, etc.
 # See https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles
 binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --run-aviary \
-  --snakemake-profile qsub --cluster-retries 3 --local-cores 64 --cores 64
+  --snakemake-profile qsub --local-cores 64 --cores 64
 ```
 
 Important options: