Add option to manually set extra apptainer bind points

stemcnv_check/__main__.py

@@ -62,6 +62,10 @@ def setup_argparse():
     group_snake.add_argument('--no-cache', action='store_true',
                              help="Do not use a chache directory. The cache is used for workflow created metadata "
                              "(conda envs, singularity images, and VEP data). The default cache path is defined in the conifg file.")
+    group_snake.add_argument('--bind-points',
+                             help="Additional bind points for apptainer containers, intended for expter users. "
+                                  "Use i.e. '/path' to make it availbale in apptainer, useful in case local directory "
+                                  "contains symlinks that won't resolve in the container.")
 
     group_snake.add_argument('--target', '-t', default='complete',
                              choices=('complete', 'report', 'collate-summary', 'summary-tables', 'collate-cnv-calls',

stemcnv_check/app/make_staticdata.py

@@ -153,7 +153,9 @@ def run_staticdata_workflow(args, array_name):
                             deployment_method=DeploymentMethod.parse_choices_set(['conda', 'apptainer']),
                             conda_prefix=cache_path,
                             apptainer_prefix=cache_path,
-                            apptainer_args=make_apptainer_args(config, cache_path, not_existing_ok=True),
+                            apptainer_args=make_apptainer_args(
+                                config, cache_path, not_existing_ok=True, extra_bind_args=args.bind_points
+                            ),
                         ),
                     )
                     .dag(
@@ -191,7 +193,9 @@ def run_staticdata_workflow(args, array_name):
                     deployment_method=DeploymentMethod.parse_choices_set(['conda', 'apptainer']),
                     conda_prefix=cache_path,
                     apptainer_prefix=cache_path,
-                    apptainer_args=make_apptainer_args(config, cache_path, tmpdir=tmpdir, not_existing_ok=True),
+                    apptainer_args=make_apptainer_args(
+                        config, cache_path, tmpdir=tmpdir, not_existing_ok=True, extra_bind_args=args.bind_points
+                    ),
                 )
             )
             .dag(

stemcnv_check/app/run_workflow.py

@@ -16,7 +16,7 @@ def run_stemcnv_check_workflow(args):
         "-s", str(importlib.resources.files(STEM_CNV_CHECK).joinpath('rules', 'StemCNV-check.smk')),
         "--printshellcmds", "--rerun-incomplete",
         "--sdm", "conda", "apptainer",
-        "--apptainer-args", make_apptainer_args(config, cache_path),
+        "--apptainer-args", make_apptainer_args(config, cache_path, extra_bind_args=args.bind_points),
         #"--conda-frontend", args.conda_frontend,
         ]
     if args.directory:

stemcnv_check/helpers.py

@@ -67,7 +67,7 @@ def rename_func(name): return name
         return sample_tb.set_index('Sample_ID', drop=False)
 
 
-def make_apptainer_args(config, cache_path, tmpdir=None, not_existing_ok=False):
+def make_apptainer_args(config, cache_path, tmpdir=None, not_existing_ok=False, extra_bind_args=None):
     """Collect all outside filepaths that need to be bound inside container"""
 
     bind_points = [
@@ -106,6 +106,12 @@ def make_apptainer_args(config, cache_path, tmpdir=None, not_existing_ok=False):
 
     # Sort bind_points to make testing easier (loops over config_dict add them in a non-deterministic order)
     bind_point_str = "-B " + ','.join(f"'{host}':'{cont}'" for host, cont in sorted(bind_points, key=lambda x: x[1]))
+    # allow additional arguments to be passed
+    if extra_bind_args:
+        if isinstance(extra_bind_args, str):
+            extra_bind_args = [extra_bind_args]
+        bind_point_str = bind_point_str + ',' + ','.join(list(extra_bind_args))
+
     logging.debug("Binding points for apptainer: " + str(bind_point_str))
 
     return bind_point_str

tests/test_helpers.py

@@ -167,6 +167,9 @@ def get_expected(extra=[]):
     expected = get_expected(expected_extra + ["'relative/bpm_manifest.bpm':'/outside/ExampleArray/bpm_manifest.bpm'"])
     assert expected == helpers.make_apptainer_args(config, None)
 
+    # test with direct addition
+    assert expected+',/abcdef' == helpers.make_apptainer_args(config, None, extra_bind_args='/abcdef')
+
     # test with cache_path & auto-creation of global paths
     cache_path = '/path/to/cache'
     config['global_settings'] = {