fix: update biowulf scheduler interactions for lscratch

scripts/config.py

@@ -4,7 +4,7 @@
 import logging
 from pathlib import Path
 from os import access as check_access, R_OK
-from os.path import expandvars
+from os.path import expandvars, expanduser
 from socket import gethostname
 from uuid import uuid4
 from collections import defaultdict
@@ -161,18 +161,11 @@ def get_tmp_dir(host):
 
     this_tmp = TMP_CONFIGS[host]['user']
 
-    try:
-        Path(expandvars(this_tmp)).mkdir(parents=False, exist_ok=True)
-    except Exception as e:
-        logging.error("SLURM TMP DIR NOT FOUND: " + traceback.format_exc())
-        this_tmp = TMP_CONFIGS[host]['global']
-
-    try:
-        Path(expandvars(this_tmp)).mkdir(parents=False, exist_ok=True)
-    except:
-        raise OSError(f'TMPDIR does exist and can not be created: "{this_tmp}"')
-
-    return this_tmp
+    # this directory, if it does not exist, 
+    if Path(this_tmp).parents[0].exists():
+        return this_tmp
+    else:
+        return TMP_CONFIGS[host]['global']
 
 
 DIRECTORY_CONFIGS = {

scripts/utils.py

@@ -188,13 +188,6 @@ def get_mods(init=False):
 def get_mounts(*extras):
     mount_binds = []
     resources = get_resource_config()
-    slurm_id = os.environ
-
-    if os.environ.get("SLURM_JOB_ID", None):
-        tmpdir = get_tmp_dir(get_current_server())
-        if not Path(os.path.expandvars(tmpdir)).exists():
-            Path(tmpdir).mkdir(parents=True, exist_ok=True)
-        mount_binds.append(str(tmpdir) + ':/tmp:rw')
 
     if resources:
         for this_mount_label, this_mount_attrs in resources['mounts'].items():
@@ -227,6 +220,8 @@ def get_mounts(*extras):
                 raise FileNotFoundError(f"Can't mount {str(bind)}, it doesn't exist!")
             file_to, file_from, mode = str(bind), str(bind), 'rw'
         mounts.append(file_from + ':' + file_to + ':' + mode)
+
+    mounts.append('\$TMPDIR:/tmp:rw')
 
     return ','.join(mounts)
 

workflow/demux.smk

@@ -36,6 +36,7 @@ rule bcl2fastq:
     threads: 34
     resources: 
         mem_mb = int(64e3),
+        runtime = 4*60,
     shell: 
         """
             bcl2fastq \
@@ -94,6 +95,7 @@ rule bclconvert:
     threads: 50
     resources: 
         mem_mb = int(64e3),
+        runtime = 4*60,
     shell:
         """
         bcl-convert \