Fix other paths so /tmp is clear.

Author: Peter Amstutz

cwltool/pathmapper.py

@@ -58,11 +58,11 @@ def __init__(self, referenced_files, basedir):
 
         names = set()
         for d in self.dirs:
-            name = os.path.join("/tmp", prefix + os.path.basename(d))
+            name = os.path.join("/var/lib/cwl", prefix + os.path.basename(d))
             i = 1
             while name in names:
                 i += 1
-                name = os.path.join("/tmp", prefix + os.path.basename(d) + str(i))
+                name = os.path.join("/var/lib/cwl", prefix + os.path.basename(d) + str(i))
             names.add(name)
             self.dirs[d] = name
 

cwltool/process.py

@@ -253,8 +253,8 @@ def _init_job(self, joborder, input_basedir, **kwargs):
 
         dockerReq, _ = self.get_requirement("DockerRequirement")
         if dockerReq and kwargs.get("use_container"):
-            builder.outdir = kwargs.get("docker_outdir") or "/tmp/job_output"
-            builder.tmpdir = kwargs.get("docker_tmpdir") or "/tmp/job_tmp"
+            builder.outdir = kwargs.get("docker_outdir") or "/var/spool/cwl"
+            builder.tmpdir = kwargs.get("docker_tmpdir") or "/tmp"
         else:
             builder.outdir = kwargs.get("outdir") or tempfile.mkdtemp()
             builder.tmpdir = kwargs.get("tmpdir") or tempfile.mkdtemp()