Exposing snakemake's --rerun-triggers (#170).

requirements/base.txt

@@ -12,7 +12,7 @@ biomedsheets >=0.11.1
 termcolor==1.1.0
 
 # Snakemake is used for providing the actual wrapper calling functionality
-snakemake >=7.0.2
+snakemake >=7.8.0
 # Snakemake needs manual install of PyYAML to make YAML configuration loading work
 PyYAML>=3.12
 

snappy_pipeline/apps/snappy_snake.py

@@ -13,6 +13,7 @@
 import sys
 
 from ruamel import yaml
+from snakemake import RERUN_TRIGGERS
 from snakemake import main as snakemake_main
 
 from .. import __version__
@@ -169,6 +170,8 @@ def run(wrapper_args):
     ]
     if wrapper_args.keep_going:
         snakemake_argv.append("--keep-going")
+    if wrapper_args.rerun_triggers:
+        snakemake_argv += ["--rerun-triggers"] + wrapper_args.rerun_triggers
     if wrapper_args.unlock:
         snakemake_argv.append("--unlock")
     if wrapper_args.rerun_incomplete:
@@ -285,6 +288,13 @@ def main(argv=None):
             "not yet exist."
         ),
     )
+    group.add_argument(
+        "--rerun-triggers",
+        nargs="+",
+        choices=RERUN_TRIGGERS,
+        default=["mtime"],  # TODO: switch to RERUN_TRIGGERS,
+        help="Expose --rerun-triggers from snakemake but set to only mtime by default.",
+    )
 
     group = parser.add_argument_group(
         "Snakemake Verbosity / Debugging",

tests/snappy_pipeline/apps/test_snappy_snake.py

@@ -46,6 +46,8 @@ def test_snappy_snake_list_output(germline_sheet_fake_project_ngs_mapping_fs, mo
             p + "/workflows/ngs_mapping/Snakefile",
             "--jobscript",
             p + "/apps/tpls/jobscript.sh",
+            "--rerun-triggers",
+            "mtime",
             "-S",
             "--verbose",
             "--cores",