From 4ad917d47720e1ed4a814ef6348b01e7685e0654 Mon Sep 17 00:00:00 2001
From: Marcel Zwiers <m.zwiers@donders.ru.nl>
Date: Mon, 24 Jun 2024 14:50:00 +0200
Subject: [PATCH] Minor tweak

---
 bidscoin/bcoin.py                | 20 ++++++++++++--------
 bidscoin/bidsapps/slicereport.py |  4 ++--
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/bidscoin/bcoin.py b/bidscoin/bcoin.py
index b604a4d8..9a6533d9 100755
--- a/bidscoin/bcoin.py
+++ b/bidscoin/bcoin.py
@@ -60,14 +60,18 @@ def drmaa_nativespec(specs: str, session) -> str:
     :return:        The converted native specifications
     """
 
-    jobmanager = session.drmaaImplementation
-
-    if 'Slurm' in jobmanager and '-l ' in specs:
-        specs = (specs.replace('-l ', '')
-                      .replace(',', ' ')
-                      .replace('walltime', '--time')
-                      .replace('mem', '--mem')
-                      .replace('gb','000'))
+    jobmanager: str = session.drmaaImplementation
+
+    if '-l ' in specs and 'torque' not in jobmanager.lower():
+
+        if 'slurm' in jobmanager.lower():
+            specs = (specs.replace('-l ', '')
+                          .replace(',', ' ')
+                          .replace('walltime', '--time')
+                          .replace('mem', '--mem')
+                          .replace('gb','000'))
+        else:
+            LOGGER.warning(f"Default native specifications not (yet) provided for {jobmanager}")
 
     return specs.strip()
 
diff --git a/bidscoin/bidsapps/slicereport.py b/bidscoin/bidsapps/slicereport.py
index b33b698b..07fd8f89 100755
--- a/bidscoin/bidsapps/slicereport.py
+++ b/bidscoin/bidsapps/slicereport.py
@@ -109,7 +109,7 @@ 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"rm -r {workdir}" if not DEBUG else '')
+               + (f"cd {workdir.parent}; rm -r {workdir}" if not DEBUG else '')
 
     # Run the command on the HPC cluster or directly in the shell
     if cluster:
@@ -129,7 +129,7 @@ def slicer_append(inputimage: Path, operations: str, outlineimage: Path, mainopt
             jt.outputPath          = f"{os.getenv('HOSTNAME')}:{workdir if DEBUG else tempfile.gettempdir()}/{jt.jobName}.out"
             jobid                  = pbatch.runJob(jt)
             pbatch.deleteJobTemplate(jt)
-            LOGGER.info(f"Your slicereport job has been submitted with ID: {jobid}")
+            LOGGER.verbose(f"Your slicereport job has been submitted with ID: {jobid}")
 
     else:
         LOGGER.bcdebug(f"Command: {command}")