Minor tweak

bidscoin/bcoin.py

@@ -53,16 +53,16 @@ def update_to(self, b=1, bsize=1, tsize=None):
 
 def drmaa_nativespec(specs: str, session) -> str:
     """
-    Converts native Torque walltime and memory specifications to the DRMAA implementation (currently only Slurm is supported)
+    Converts (CLI default) native Torque walltime and memory specifications to the DRMAA implementation (currently only Slurm is supported)
 
-    :param specs:   Native Torque walltime and memory specifications, e.g. '-l walltime=00:10:00,mem=2gb'
+    :param specs:   Native Torque walltime and memory specifications, e.g. '-l walltime=00:10:00,mem=2gb' from argparse CLI
     :param session: The DRMAA session
     :return:        The converted native specifications
     """
 
     jobmanager: str = session.drmaaImplementation
 
-    if '-l ' in specs and 'torque' not in jobmanager.lower():
+    if '-l ' in specs and 'pbs' not in jobmanager.lower():
 
         if 'slurm' in jobmanager.lower():
             specs = (specs.replace('-l ', '')

bidscoin/bidsapps/slicereport.py

@@ -109,20 +109,17 @@ def slicer_append(inputimage: Path, operations: str, outlineimage: Path, mainopt
                f"slicer {'mathsimg' if mathsimg else inputimage} {outlineimage if outlineimage.name else ''} {mainopts} {outputopts}\n" \
                f"pngappend {sliceroutput} {montage.name}\n" \
                f"mv {montage.name} {montage.parent}\n" \
-               + (f"cd {workdir.parent}; rm -r {workdir}" if not DEBUG else '')
+               + (f"rm -r {workdir}" if not DEBUG else '')
 
     # Run the command on the HPC cluster or directly in the shell
     if cluster:
         from drmaa import Session as drmaasession   # Lazy import to avoid import error on non-HPC systems
         from bidscoin.bcoin import drmaa_nativespec
 
-        script = workdir/'slicereport.sh'
-        script.write_text('#!/bin/bash\n' + command)
-        script.chmod(0o744)
         with drmaasession() as pbatch:
             jt                     = pbatch.createJobTemplate()
             jt.jobEnvironment      = os.environ
-            jt.remoteCommand       = str(script)
+            jt.remoteCommand       = '#!/bin/bash\n' + command
             jt.nativeSpecification = drmaa_nativespec(cluster, pbatch)
             jt.joinFiles           = True
             jt.jobName             = 'slicereport'