diff --git a/cwltool.py b/cwltool.py
index a3b9c6928..0cdd91a14 100755
--- a/cwltool.py
+++ b/cwltool.py
@@ -6,6 +6,7 @@
 """
 
 import sys
+
 from cwltool import main
 
 if __name__ == "__main__":
diff --git a/cwltool/__main__.py b/cwltool/__main__.py
index 2b15c84f5..4d84a444f 100644
--- a/cwltool/__main__.py
+++ b/cwltool/__main__.py
@@ -1,4 +1,5 @@
-from . import main
 import sys
 
+from . import main
+
 sys.exit(main.main())
diff --git a/cwltool/builder.py b/cwltool/builder.py
index 40cb789bd..595bdbdea 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -1,13 +1,15 @@
 import copy
-from .utils import aslist
-from . import expression
+
 import avro
 import schema_salad.validate as validate
 from schema_salad.sourceline import SourceLine
 from typing import Any, Callable, Text, Type, Union
+
+from . import expression
 from .errors import WorkflowException
+from .pathmapper import PathMapper, adjustFileObjs, normalizeFilesDirs
 from .stdfsaccess import StdFsAccess
-from .pathmapper import PathMapper, adjustFileObjs, adjustDirObjs, normalizeFilesDirs
+from .utils import aslist
 
 CONTENT_LIMIT = 64 * 1024
 
@@ -18,8 +20,8 @@ def substitute(value, replace):  # type: (Text, Text) -> Text
     else:
         return value + replace
 
-class Builder(object):
 
+class Builder(object):
     def __init__(self):  # type: () -> None
         self.names = None  # type: avro.schema.Names
         self.schemaDefs = None  # type: Dict[Text, Dict[Text, Any]]
@@ -39,8 +41,12 @@ def __init__(self):  # type: () -> None
         self.build_job_script = None  # type: Callable[[List[str]], Text]
         self.debug = False  # type: bool
 
-    def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
+    def bind_input(self, schema, datum, lead_pos=None, tail_pos=None):
         # type: (Dict[Text, Any], Any, Union[int, List[int]], List[int]) -> List[Dict[Text, Any]]
+        if tail_pos is None:
+            tail_pos = []
+        if lead_pos is None:
+            lead_pos = []
         bindings = []  # type: List[Dict[Text,Text]]
         binding = None  # type: Dict[Text,Any]
         if "inputBinding" in schema and isinstance(schema["inputBinding"], dict):
@@ -137,7 +143,6 @@ def _capture_files(f):
             if schema["type"] == "Directory":
                 self.files.append(datum)
 
-
         # Position to front of the sort key
         if binding:
             for bi in bindings:
@@ -198,7 +203,7 @@ def do_eval(self, ex, context=None, pull_image=True, recursive=False):
         # type: (Union[Dict[Text, Text], Text], Any, bool, bool) -> Any
         if recursive:
             if isinstance(ex, dict):
-                return {k: self.do_eval(v, context, pull_image, recursive) for k,v in ex.iteritems()}
+                return {k: self.do_eval(v, context, pull_image, recursive) for k, v in ex.iteritems()}
             if isinstance(ex, list):
                 return [self.do_eval(v, context, pull_image, recursive) for v in ex]
 
diff --git a/cwltool/cwlrdf.py b/cwltool/cwlrdf.py
index 950357b06..af94966b6 100644
--- a/cwltool/cwlrdf.py
+++ b/cwltool/cwlrdf.py
@@ -1,11 +1,12 @@
-import json
 import urlparse
-from .process import Process
-from schema_salad.ref_resolver import Loader, ContextType
+
+from rdflib import Graph
 from schema_salad.jsonld_context import makerdf
-from rdflib import Graph, plugin, URIRef
-from rdflib.serializer import Serializer
-from typing import Any, Dict, IO, Text, Union
+from schema_salad.ref_resolver import ContextType
+from typing import Any, Dict, IO, Text
+
+from .process import Process
+
 
 def gather(tool, ctx):  # type: (Process, ContextType) -> Graph
     g = Graph()
@@ -16,14 +17,16 @@ def visitor(t):
     tool.visit(visitor)
     return g
 
+
 def printrdf(wf, ctx, sr, stdout):
     # type: (Process, ContextType, Text, IO[Any]) -> None
     stdout.write(gather(wf, ctx).serialize(format=sr))
 
+
 def lastpart(uri):  # type: (Any) -> Text
     uri = Text(uri)
     if "/" in uri:
-        return uri[uri.rindex("/")+1:]
+        return uri[uri.rindex("/") + 1:]
     else:
         return uri
 
@@ -84,6 +87,7 @@ def dot_with_parameters(g, stdout):  # type: (Graph, IO[Any]) -> None
     for (inp,) in qres:
         stdout.write(u'"%s" [shape=octagon]\n' % (lastpart(inp)))
 
+
 def dot_without_parameters(g, stdout):  # type: (Graph, IO[Any]) -> None
     dotname = {}  # type: Dict[Text,Text]
     clusternode = {}
@@ -163,7 +167,7 @@ def printdot(wf, ctx, stdout, include_parameters=False):
 
     stdout.write("digraph {")
 
-    #g.namespace_manager.qname(predicate)
+    # g.namespace_manager.qname(predicate)
 
     if include_parameters:
         dot_with_parameters(g, stdout)
diff --git a/cwltool/docker.py b/cwltool/docker.py
index 812852ff9..0b9ef202b 100644
--- a/cwltool/docker.py
+++ b/cwltool/docker.py
@@ -1,15 +1,18 @@
-import subprocess
 import logging
-import sys
-import requests
 import os
-from .errors import WorkflowException
 import re
+import subprocess
+import sys
 import tempfile
-from typing import Any, Text, Union
+
+import requests
+from typing import Text
+
+from .errors import WorkflowException
 
 _logger = logging.getLogger("cwltool")
 
+
 def get_image(dockerRequirement, pull_image, dry_run=False):
     # type: (Dict[Text, Text], bool, bool) -> bool
     found = False
@@ -44,7 +47,7 @@ def get_image(dockerRequirement, pull_image, dry_run=False):
             with open(os.path.join(dockerfile_dir, "Dockerfile"), "w") as df:
                 df.write(dockerRequirement["dockerFile"])
             cmd = ["docker", "build", "--tag=%s" %
-                str(dockerRequirement["dockerImageId"]), dockerfile_dir]
+                   str(dockerRequirement["dockerImageId"]), dockerfile_dir]
             _logger.info(Text(cmd))
             if not dry_run:
                 subprocess.check_call(cmd, stdout=sys.stderr)
@@ -62,7 +65,7 @@ def get_image(dockerRequirement, pull_image, dry_run=False):
                     _logger.info(u"Sending GET request to %s", dockerRequirement["dockerLoad"])
                     req = requests.get(dockerRequirement["dockerLoad"], stream=True)
                     n = 0
-                    for chunk in req.iter_content(1024*1024):
+                    for chunk in req.iter_content(1024 * 1024):
                         n += len(chunk)
                         _logger.info("\r%i bytes" % (n))
                         loadproc.stdin.write(chunk)
@@ -73,7 +76,7 @@ def get_image(dockerRequirement, pull_image, dry_run=False):
                 found = True
         elif "dockerImport" in dockerRequirement:
             cmd = ["docker", "import", str(dockerRequirement["dockerImport"]),
-                str(dockerRequirement["dockerImageId"])]
+                   str(dockerRequirement["dockerImageId"])]
             _logger.info(Text(cmd))
             if not dry_run:
                 subprocess.check_call(cmd, stdout=sys.stderr)
diff --git a/cwltool/docker_uid.py b/cwltool/docker_uid.py
index 11223c74b..5b63e833d 100644
--- a/cwltool/docker_uid.py
+++ b/cwltool/docker_uid.py
@@ -1,5 +1,6 @@
 import subprocess
-from typing import Text, Union
+
+from typing import Text
 
 
 def docker_vm_uid():  # type: () -> int
diff --git a/cwltool/draft2tool.py b/cwltool/draft2tool.py
index 9ca34d6db..54590a84b 100644
--- a/cwltool/draft2tool.py
+++ b/cwltool/draft2tool.py
@@ -1,32 +1,28 @@
-import shutil
-from functools import partial
-import json
 import copy
-import os
-import glob
-import logging
 import hashlib
+import json
+import logging
+import os
 import re
-import urlparse
+import shutil
 import tempfile
-import errno
+import urlparse
+from functools import partial
 
-import avro.schema
 import schema_salad.validate as validate
-from schema_salad.ref_resolver import file_uri, uri_file_path
 import shellescape
+from schema_salad.ref_resolver import file_uri, uri_file_path
+from schema_salad.sourceline import SourceLine, indent
 from typing import Any, Callable, cast, Generator, Text, Union
 
-from .process import Process, shortname, uniquename, getListing, normalizeFilesDirs, compute_checksums
+from .builder import CONTENT_LIMIT, substitute, Builder, adjustFileObjs
+from .pathmapper import adjustDirObjs
 from .errors import WorkflowException
-from .utils import aslist
-from . import expression
-from .builder import CONTENT_LIMIT, substitute, Builder, adjustFileObjs, adjustDirObjs
-from .pathmapper import PathMapper
 from .job import CommandLineJob
+from .pathmapper import PathMapper
+from .process import Process, shortname, uniquename, getListing, normalizeFilesDirs, compute_checksums
 from .stdfsaccess import StdFsAccess
-
-from schema_salad.sourceline import SourceLine, indent
+from .utils import aslist
 
 ACCEPTLIST_EN_STRICT_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
 ACCEPTLIST_EN_RELAXED_RE = re.compile(r"^[ a-zA-Z0-9._+-]+$")  # with spaces
@@ -36,6 +32,7 @@
 
 _logger = logging.getLogger("cwltool")
 
+
 class ExpressionTool(Process):
     def __init__(self, toolpath_object, **kwargs):
         # type: (Dict[Text, Any], **Any) -> None
@@ -60,7 +57,7 @@ def run(self, **kwargs):  # type: (**Any) -> None
                 self.output_callback(ev, "success")
             except Exception as e:
                 _logger.warn(u"Failed to evaluate expression:\n%s",
-                        e, exc_info=kwargs.get('debug'))
+                             e, exc_info=kwargs.get('debug'))
                 self.output_callback({}, "permanentFail")
 
     def job(self, joborder, output_callback, **kwargs):
@@ -83,6 +80,7 @@ def remove_path(f):  # type: (Dict[Text, Any]) -> None
     if "path" in f:
         del f["path"]
 
+
 def revmap_file(builder, outdir, f):
     # type: (Builder, Text, Dict[Text, Any]) -> Union[Dict[Text, Any], None]
 
@@ -104,7 +102,7 @@ def revmap_file(builder, outdir, f):
             if revmap_f:
                 f["location"] = revmap_f[1]
             elif path.startswith(builder.outdir):
-                f["location"] = builder.fs_access.join(outdir, path[len(builder.outdir)+1:])
+                f["location"] = builder.fs_access.join(outdir, path[len(builder.outdir) + 1:])
         return f
 
     if "path" in f:
@@ -115,10 +113,11 @@ def revmap_file(builder, outdir, f):
             f["location"] = revmap_f[1]
             return f
         elif path.startswith(builder.outdir):
-            f["location"] = builder.fs_access.join(outdir, path[len(builder.outdir)+1:])
+            f["location"] = builder.fs_access.join(outdir, path[len(builder.outdir) + 1:])
             return f
         else:
-            raise WorkflowException(u"Output file path %s must be within designated output directory (%s) or an input file pass through." % (path, builder.outdir))
+            raise WorkflowException(u"Output file path %s must be within designated output directory (%s) or an input "
+                                    u"file pass through." % (path, builder.outdir))
 
     raise WorkflowException(u"Output File object is missing both `location` and `path` fields: %s" % f)
 
@@ -139,6 +138,7 @@ def run(self, **kwargs):
             self.outdir,
             kwargs.get("compute_checksum", True)), "success")
 
+
 # map files to assigned path inside a container. We need to also explicitly
 # walk over input as implicit reassignment doesn't reach everything in builder.bindings
 def check_adjust(builder, f):
@@ -151,6 +151,7 @@ def check_adjust(builder, f):
         raise WorkflowException("Invalid filename: '%s' contains illegal characters" % (f["basename"]))
     return f
 
+
 class CommandLineTool(Process):
     def __init__(self, toolpath_object, **kwargs):
         # type: (Dict[Text, Any], **Any) -> None
@@ -191,7 +192,7 @@ def job(self, joborder, output_callback, **kwargs):
                 cmdline = ["docker", "run", dockerimg] + cmdline
             keydict = {u"cmdline": cmdline}
 
-            for _,f in cachebuilder.pathmapper.items():
+            for _, f in cachebuilder.pathmapper.items():
                 if f.type == "File":
                     st = os.stat(f.resolved)
                     keydict[f.resolved] = [st.st_size, int(st.st_mtime * 1000)]
@@ -205,11 +206,11 @@ def job(self, joborder, output_callback, **kwargs):
                     if r["class"] in interesting and r["class"] not in keydict:
                         keydict[r["class"]] = r
 
-            keydictstr = json.dumps(keydict, separators=(',',':'), sort_keys=True)
+            keydictstr = json.dumps(keydict, separators=(',', ':'), sort_keys=True)
             cachekey = hashlib.md5(keydictstr).hexdigest()
 
             _logger.debug("[job %s] keydictstr is %s -> %s", jobname,
-                    keydictstr, cachekey)
+                          keydictstr, cachekey)
 
             jobcache = os.path.join(kwargs["cachedir"], cachekey)
             jobcachepending = jobcache + ".pending"
@@ -235,11 +236,12 @@ def rm_pending_output_callback(output_callback, jobcachepending,
                     if processStatus == "success":
                         os.remove(jobcachepending)
                     output_callback(outputs, processStatus)
+
                 output_callback = cast(
                     Callable[..., Any],  # known bug in mypy
                     # https://github.com/python/mypy/issues/797
                     partial(rm_pending_output_callback, output_callback,
-                        jobcachepending))
+                            jobcachepending))
 
         builder = self._init_job(joborder, **kwargs)
 
@@ -260,12 +262,11 @@ def rm_pending_output_callback(output_callback, jobcachepending,
 
         if _logger.isEnabledFor(logging.DEBUG):
             _logger.debug(u"[job %s] initializing from %s%s",
-                         j.name,
-                         self.tool.get("id", ""),
-                         u" as part of %s" % kwargs["part_of"] if "part_of" in kwargs else "")
+                          j.name,
+                          self.tool.get("id", ""),
+                          u" as part of %s" % kwargs["part_of"] if "part_of" in kwargs else "")
             _logger.debug(u"[job %s] %s", j.name, json.dumps(joborder, indent=4))
 
-
         builder.pathmapper = None
         make_path_mapper_kwargs = kwargs
         if "stagedir" in make_path_mapper_kwargs:
@@ -275,7 +276,8 @@ def rm_pending_output_callback(output_callback, jobcachepending,
         builder.requirements = j.requirements
 
         if _logger.isEnabledFor(logging.DEBUG):
-            _logger.debug(u"[job %s] path mappings is %s", j.name, json.dumps({p: builder.pathmapper.mapper(p) for p in builder.pathmapper.files()}, indent=4))
+            _logger.debug(u"[job %s] path mappings is %s", j.name,
+                          json.dumps({p: builder.pathmapper.mapper(p) for p in builder.pathmapper.files()}, indent=4))
 
         _check_adjust = partial(check_adjust, builder)
 
@@ -334,7 +336,7 @@ def rm_pending_output_callback(output_callback, jobcachepending,
                         ls.append(et)
                     else:
                         ls.append(builder.do_eval(t))
-            for i,t in enumerate(ls):
+            for i, t in enumerate(ls):
                 if "entry" in t:
                     if isinstance(t["entry"], basestring):
                         ls[i] = {
@@ -381,8 +383,9 @@ def rm_pending_output_callback(output_callback, jobcachepending,
 
     def collect_output_ports(self, ports, builder, outdir, compute_checksum=True):
         # type: (Set[Dict[Text, Any]], Builder, Text, bool) -> Dict[Text, Union[Text, List[Any], Dict[Text, Any]]]
+        ret = {}  # type: Dict[Text, Union[Text, List[Any], Dict[Text, Any]]]
         try:
-            ret = {}  # type: Dict[Text, Union[Text, List[Any], Dict[Text, Any]]]
+
             fs_access = builder.make_fs_access(outdir)
             custom_output = fs_access.join(outdir, "cwl.output.json")
             if fs_access.exists(custom_output):
@@ -395,7 +398,8 @@ def collect_output_ports(self, ports, builder, outdir, compute_checksum=True):
                     with SourceLine(ports, i, WorkflowException):
                         fragment = shortname(port["id"])
                         try:
-                            ret[fragment] = self.collect_output(port, builder, outdir, fs_access, compute_checksum=compute_checksum)
+                            ret[fragment] = self.collect_output(port, builder, outdir, fs_access,
+                                                                compute_checksum=compute_checksum)
                         except Exception as e:
                             _logger.debug(
                                 u"Error collecting output for parameter '%s'"
@@ -406,9 +410,9 @@ def collect_output_ports(self, ports, builder, outdir, compute_checksum=True):
 
             if ret:
                 adjustFileObjs(ret,
-                        cast(Callable[[Any], Any],  # known bug in mypy
-                            # https://github.com/python/mypy/issues/797
-                            partial(revmap_file, builder, outdir)))
+                               cast(Callable[[Any], Any],  # known bug in mypy
+                                    # https://github.com/python/mypy/issues/797
+                                    partial(revmap_file, builder, outdir)))
                 adjustFileObjs(ret, remove_path)
                 adjustDirObjs(ret, remove_path)
                 normalizeFilesDirs(ret)
@@ -438,7 +442,7 @@ def collect_output(self, schema, builder, outdir, fs_access, compute_checksum=Tr
 
                     for gb in globpatterns:
                         if gb.startswith(outdir):
-                            gb = gb[len(outdir)+1:]
+                            gb = gb[len(outdir) + 1:]
                         elif gb == ".":
                             gb = outdir
                         elif gb.startswith("/"):
@@ -464,7 +468,7 @@ def collect_output(self, schema, builder, outdir, fs_access, compute_checksum=Tr
                                 checksum = hashlib.sha1()
                                 while contents != "":
                                     checksum.update(contents)
-                                    contents = f.read(1024*1024)
+                                    contents = f.read(1024 * 1024)
                                 files["checksum"] = "sha1$%s" % checksum.hexdigest()
                             f.seek(0, 2)
                             filesize = f.tell()
@@ -523,8 +527,7 @@ def collect_output(self, schema, builder, outdir, fs_access, compute_checksum=Tr
             if not r and optional:
                 r = None
 
-        if (not r and isinstance(schema["type"], dict) and
-                schema["type"]["type"] == "record"):
+        if (not r and isinstance(schema["type"], dict) and schema["type"]["type"] == "record"):
             out = {}
             for f in schema["type"]["fields"]:
                 out[shortname(f["name"])] = self.collect_output(  # type: ignore
diff --git a/cwltool/errors.py b/cwltool/errors.py
index 6bf187cf2..9df1236fa 100644
--- a/cwltool/errors.py
+++ b/cwltool/errors.py
@@ -1,5 +1,6 @@
 class WorkflowException(Exception):
     pass
 
+
 class UnsupportedRequirement(WorkflowException):
     pass
diff --git a/cwltool/expression.py b/cwltool/expression.py
index 96cbe99fe..72e4d449f 100644
--- a/cwltool/expression.py
+++ b/cwltool/expression.py
@@ -1,21 +1,16 @@
-import subprocess
+import copy
 import json
 import logging
-import os
 import re
-import copy
 
 from typing import Any, AnyStr, Union, Text, Dict, List
-import schema_salad.validate as validate
-import schema_salad.ref_resolver
 
-from .utils import aslist, get_feature
-from .errors import WorkflowException
 from . import sandboxjs
-from . import docker
+from .errors import WorkflowException
 
 _logger = logging.getLogger("cwltool")
 
+
 def jshead(engineConfig, rootvars):
     # type: (List[Text], Dict[Text, Any]) -> Text
     return u"\n".join(engineConfig + [u"var %s = %s;" % (k, json.dumps(v, indent=4)) for k, v in rootvars.items()])
@@ -29,11 +24,13 @@ def jshead(engineConfig, rootvars):
 segment_re = re.compile(segments, flags=re.UNICODE)
 param_re = re.compile(r"\((%s)%s*\)$" % (seg_symbol, segments), flags=re.UNICODE)
 
-JSON = Union[Dict[Any,Any], List[Any], Text, int, long, float, bool, None]
+JSON = Union[Dict[Any, Any], List[Any], Text, int, long, float, bool, None]
+
 
 class SubstitutionError(Exception):
     pass
 
+
 def scanner(scan):  # type: (Text) -> List[int]
     DEFAULT = 0
     DOLLAR = 1
@@ -58,13 +55,13 @@ def scanner(scan):  # type: (Text) -> List[int]
         elif state == BACKSLASH:
             stack.pop()
             if stack[-1] == DEFAULT:
-                return [i-1, i+1]
+                return [i - 1, i + 1]
         elif state == DOLLAR:
             if c == '(':
-                start = i-1
+                start = i - 1
                 stack.append(PAREN)
             elif c == '{':
-                start = i-1
+                start = i - 1
                 stack.append(BRACE)
             else:
                 stack.pop()
@@ -74,7 +71,7 @@ def scanner(scan):  # type: (Text) -> List[int]
             elif c == ')':
                 stack.pop()
                 if stack[-1] == DOLLAR:
-                    return [start, i+1]
+                    return [start, i + 1]
             elif c == "'":
                 stack.append(SINGLE_QUOTE)
             elif c == '"':
@@ -85,7 +82,7 @@ def scanner(scan):  # type: (Text) -> List[int]
             elif c == '}':
                 stack.pop()
                 if stack[-1] == DOLLAR:
-                    return [start, i+1]
+                    return [start, i + 1]
             elif c == "'":
                 stack.append(SINGLE_QUOTE)
             elif c == '"':
@@ -103,10 +100,12 @@ def scanner(scan):  # type: (Text) -> List[int]
         i += 1
 
     if len(stack) > 1:
-        raise SubstitutionError("Substitution error, unfinished block starting at position {}: {}".format(start, scan[start:]))
+        raise SubstitutionError(
+            "Substitution error, unfinished block starting at position {}: {}".format(start, scan[start:]))
     else:
         return None
 
+
 def next_seg(remain, obj):  # type: (Text, Any) -> Any
     if remain:
         m = segment_re.match(remain)
@@ -139,6 +138,7 @@ def next_seg(remain, obj):  # type: (Text, Any) -> Any
     else:
         return obj
 
+
 def evaluator(ex, jslib, obj, fullJS=False, timeout=None, debug=False):
     # type: (Text, Text, Dict[Text, Any], bool, int, bool) -> JSON
     m = param_re.match(ex)
@@ -150,7 +150,10 @@ def evaluator(ex, jslib, obj, fullJS=False, timeout=None, debug=False):
     elif fullJS:
         return sandboxjs.execjs(ex, jslib, timeout=timeout, debug=debug)
     else:
-        raise sandboxjs.JavascriptException("Syntax error in parameter reference '%s' or used Javascript code without specifying InlineJavascriptRequirement.", ex)
+        raise sandboxjs.JavascriptException(
+            "Syntax error in parameter reference '%s' or used Javascript code without specifying InlineJavascriptRequirement.",
+            ex)
+
 
 def interpolate(scan, rootvars,
                 timeout=None, fullJS=None, jslib="", debug=False):
@@ -162,7 +165,7 @@ def interpolate(scan, rootvars,
         parts.append(scan[0:w[0]])
 
         if scan[w[0]] == '$':
-            e = evaluator(scan[w[0]+1:w[1]], jslib, rootvars, fullJS=fullJS,
+            e = evaluator(scan[w[0] + 1:w[1]], jslib, rootvars, fullJS=fullJS,
                           timeout=timeout, debug=debug)
             if w[0] == 0 and w[1] == len(scan):
                 return e
@@ -171,7 +174,7 @@ def interpolate(scan, rootvars,
                 leaf = leaf[1:-1]
             parts.append(leaf)
         elif scan[w[0]] == '\\':
-            e = scan[w[1]-1]
+            e = scan[w[1] - 1]
             parts.append(e)
 
         scan = scan[w[1]:]
@@ -179,6 +182,7 @@ def interpolate(scan, rootvars,
     parts.append(scan)
     return ''.join(parts)
 
+
 def do_eval(ex, jobinput, requirements, outdir, tmpdir, resources,
             context=None, pull_image=True, timeout=None, debug=False):
     # type: (Union[dict, AnyStr], Dict[Text, Union[Dict, List, Text]], List[Dict[Text, Any]], Text, Text, Dict[Text, Union[int, Text]], Any, bool, int, bool) -> Any
@@ -190,7 +194,7 @@ def do_eval(ex, jobinput, requirements, outdir, tmpdir, resources,
     rootvars = {
         u"inputs": jobinput,
         u"self": context,
-        u"runtime": runtime }
+        u"runtime": runtime}
 
     if isinstance(ex, (str, Text)):
         fullJS = False
diff --git a/cwltool/factory.py b/cwltool/factory.py
index be2468b8d..eeb4a7cff 100644
--- a/cwltool/factory.py
+++ b/cwltool/factory.py
@@ -1,11 +1,13 @@
-from . import main
-from . import load_tool
-from . import workflow
 import os
-from .process import Process
+
 from typing import Any, Text, Union, Tuple
 from typing import Callable as tCallable
-import argparse
+
+from . import load_tool
+from . import main
+from . import workflow
+from .process import Process
+
 
 class WorkflowStatus(Exception):
     def __init__(self, out, status):
@@ -14,6 +16,7 @@ def __init__(self, out, status):
         self.out = out
         self.status = status
 
+
 class Callable(object):
     def __init__(self, t, factory):  # type: (Process, Factory) -> None
         self.t = t
@@ -29,6 +32,7 @@ def __call__(self, **kwargs):
         else:
             return out
 
+
 class Factory(object):
     def __init__(self, makeTool=workflow.defaultMakeTool,
                  executor=main.single_job_executor,
diff --git a/cwltool/flatten.py b/cwltool/flatten.py
index 477444aad..0e3e437ce 100644
--- a/cwltool/flatten.py
+++ b/cwltool/flatten.py
@@ -1,5 +1,6 @@
 from typing import Any, Callable, List, cast
 
+
 # http://rightfootin.blogspot.com/2006/09/more-on-python-flatten.html
 
 
diff --git a/cwltool/job.py b/cwltool/job.py
index 8b331a87c..8f1b9718a 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -1,26 +1,24 @@
-import subprocess
-import io
-import os
-import tempfile
-import glob
+import functools
 import json
 import logging
-import sys
-import requests
-from . import docker
-from .process import get_feature, empty_subtree, stageFiles
-from .errors import WorkflowException
+import os
+import re
 import shutil
 import stat
-import re
+import subprocess
+import sys
+import tempfile
+
 import shellescape
-import string
-from .docker_uid import docker_vm_uid
+from typing import (Any, Callable, Union, Iterable, MutableMapping,
+                    IO, Text, Tuple)
+
+from . import docker
 from .builder import Builder
-from typing import (Any, Callable, Union, Iterable, Mapping, MutableMapping,
-        IO, cast, Text, Tuple)
+from .docker_uid import docker_vm_uid
+from .errors import WorkflowException
 from .pathmapper import PathMapper
-import functools
+from .process import get_feature, empty_subtree, stageFiles
 
 _logger = logging.getLogger("cwltool")
 
@@ -91,8 +89,8 @@ def deref_links(outputs):  # type: (Any) -> None
         for v in outputs:
             deref_links(v)
 
-class CommandLineJob(object):
 
+class CommandLineJob(object):
     def __init__(self):  # type: () -> None
         self.builder = None  # type: Builder
         self.joborder = None  # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
@@ -121,7 +119,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
         if not os.path.exists(self.outdir):
             os.makedirs(self.outdir)
 
-        #with open(os.path.join(outdir, "cwl.input.json"), "w") as fp:
+        # with open(os.path.join(outdir, "cwl.input.json"), "w") as fp:
         #    json.dump(self.joborder, fp)
 
         runtime = []  # type: List[Text]
@@ -173,7 +171,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
 
             euid = docker_vm_uid() or os.geteuid()
 
-            if kwargs.get("no_match_user",None) is False:
+            if kwargs.get("no_match_user", None) is False:
                 runtime.append(u"--user=%s" % (euid))
 
             if rm_container:
@@ -186,7 +184,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
             # runtime.append("--env=HOME=/tmp")
             runtime.append("--env=HOME=%s" % self.builder.outdir)
 
-            for t,v in self.environment.items():
+            for t, v in self.environment.items():
                 runtime.append(u"--env=%s=%s" % (t, v))
 
             runtime.append(img_id)
@@ -216,7 +214,8 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
         _logger.info(u"[job %s] %s$ %s%s%s%s",
                      self.name,
                      self.outdir,
-                     " \\\n    ".join([shellescape.quote(Text(arg)) if shouldquote(Text(arg)) else Text(arg) for arg in (runtime + self.command_line)]),
+                     " \\\n    ".join([shellescape.quote(Text(arg)) if shouldquote(Text(arg)) else Text(arg) for arg in
+                                       (runtime + self.command_line)]),
                      u' < %s' % self.stdin if self.stdin else '',
                      u' > %s' % os.path.join(self.outdir, self.stdout) if self.stdout else '',
                      u' 2> %s' % os.path.join(self.outdir, self.stderr) if self.stderr else '')
@@ -240,6 +239,7 @@ def linkoutdir(src, tgt):
                         if src == item.resolved:
                             os.symlink(item.target, tgt)
                             break
+
                 stageFiles(generatemapper, linkoutdir)
 
             stdin_path = None
@@ -291,6 +291,7 @@ def linkoutdir(src, tgt):
                     if os.path.islink(tgt):
                         os.remove(tgt)
                         os.symlink(src, tgt)
+
                 stageFiles(generatemapper, linkoutdir, ignoreWritable=True)
 
             outputs = self.collect_outputs(self.outdir)
@@ -335,14 +336,14 @@ def linkoutdir(src, tgt):
 
 
 def _job_popen(
-    commands,  # type: List[str]
-    stdin_path,  # type: Text
-    stdout_path,  # type: Text
-    stderr_path,  # type: Text
-    env,  # type: Union[MutableMapping[Text, Text], MutableMapping[str, str]]
-    cwd,  # type: Text
-    job_dir=None,  # type: Text
-    build_job_script=None,  # type: Callable[[List[str]], Text]
+        commands,  # type: List[str]
+        stdin_path,  # type: Text
+        stdout_path,  # type: Text
+        stderr_path,  # type: Text
+        env,  # type: Union[MutableMapping[Text, Text], MutableMapping[str, str]]
+        cwd,  # type: Text
+        job_dir=None,  # type: Text
+        build_job_script=None,  # type: Callable[[List[str]], Text]
 ):
     # type: (...) -> int
 
diff --git a/cwltool/load_tool.py b/cwltool/load_tool.py
index 7096bfc68..d197aadce 100644
--- a/cwltool/load_tool.py
+++ b/cwltool/load_tool.py
@@ -1,33 +1,33 @@
 # pylint: disable=unused-import
 """Loads a CWL document."""
 
-import os
-import uuid
 import logging
+import os
 import re
 import urlparse
+import uuid
 
-from typing import Any, AnyStr, Callable, cast, Dict, Text, Tuple, Union
-from ruamel.yaml.comments import CommentedSeq, CommentedMap
-from avro.schema import Names
 import requests.sessions
-
-from schema_salad.ref_resolver import Loader, Fetcher, file_uri
-import schema_salad.validate as validate
-from schema_salad.validate import ValidationException
 import schema_salad.schema as schema
+from avro.schema import Names
+from ruamel.yaml.comments import CommentedSeq, CommentedMap
+from schema_salad.ref_resolver import Loader, Fetcher, file_uri
 from schema_salad.sourceline import cmap
+from schema_salad.validate import ValidationException
+from typing import Any, Callable, cast, Dict, Text, Tuple, Union
 
-from . import update
 from . import process
-from .process import Process, shortname
+from . import update
 from .errors import WorkflowException
+from .process import Process, shortname
 
 _logger = logging.getLogger("cwltool")
 
-def fetch_document(argsworkflow,   # type: Union[Text, dict[Text, Any]]
+
+def fetch_document(argsworkflow,  # type: Union[Text, dict[Text, Any]]
                    resolver=None,  # type: Callable[[Loader, Union[Text, dict[Text, Any]]], Text]
-                   fetcher_constructor=None  # type: Callable[[Dict[unicode, unicode], requests.sessions.Session], Fetcher]
+                   fetcher_constructor=None
+                   # type: Callable[[Dict[unicode, unicode], requests.sessions.Session], Fetcher]
                    ):
     # type: (...) -> Tuple[Loader, CommentedMap, Text]
     """Retrieve a CWL document."""
@@ -62,12 +62,13 @@ def fetch_document(argsworkflow,   # type: Union[Text, dict[Text, Any]]
 
     return document_loader, workflowobj, uri
 
+
 def _convert_stdstreams_to_files(workflowobj):
     # type: (Union[Dict[Text, Any], List[Dict[Text, Any]]]) -> None
 
     if isinstance(workflowobj, dict):
         if ('class' in workflowobj
-                and workflowobj['class'] == 'CommandLineTool'):
+            and workflowobj['class'] == 'CommandLineTool'):
             if 'outputs' in workflowobj:
                 for out in workflowobj['outputs']:
                     for streamtype in ['stdout', 'stderr']:
@@ -106,13 +107,15 @@ def _convert_stdstreams_to_files(workflowobj):
         for entry in workflowobj:
             _convert_stdstreams_to_files(entry)
 
-def validate_document(document_loader,   # type: Loader
-                      workflowobj,       # type: CommentedMap
-                      uri,               # type: Text
+
+def validate_document(document_loader,  # type: Loader
+                      workflowobj,  # type: CommentedMap
+                      uri,  # type: Text
                       enable_dev=False,  # type: bool
-                      strict=True,       # type: bool
-                      preprocess_only=False,    # type: bool
-                      fetcher_constructor=None  # type: Callable[[Dict[unicode, unicode], requests.sessions.Session], Fetcher]
+                      strict=True,  # type: bool
+                      preprocess_only=False,  # type: bool
+                      fetcher_constructor=None
+                      # type: Callable[[Dict[unicode, unicode], requests.sessions.Session], Fetcher]
                       ):
     # type: (...) -> Tuple[Loader, Names, Union[Dict[Text, Any], List[Dict[Text, Any]]], Dict[Text, Any], Text]
     """Validate a CWL document."""
@@ -159,7 +162,7 @@ def validate_document(document_loader,   # type: Loader
 
     processobj = None  # type: Union[CommentedMap, CommentedSeq, unicode]
     document_loader = Loader(sch_document_loader.ctx, schemagraph=sch_document_loader.graph,
-                  idx=document_loader.idx, cache=sch_document_loader.cache,
+                             idx=document_loader.idx, cache=sch_document_loader.cache,
                              fetcher_constructor=fetcher_constructor)
 
     workflowobj["id"] = fileuri
@@ -171,9 +174,9 @@ def validate_document(document_loader,   # type: Loader
         if not isinstance(processobj, dict):
             raise ValidationException("Draft-2 workflows must be a dict.")
         metadata = cast(CommentedMap, cmap({"$namespaces": processobj.get("$namespaces", {}),
-                         "$schemas": processobj.get("$schemas", []),
-                         "cwlVersion": processobj["cwlVersion"]},
-                        fn=fileuri))
+                                            "$schemas": processobj.get("$schemas", []),
+                                            "cwlVersion": processobj["cwlVersion"]},
+                                           fn=fileuri))
 
     _convert_stdstreams_to_files(workflowobj)
 
@@ -193,11 +196,11 @@ def validate_document(document_loader,   # type: Loader
 
 
 def make_tool(document_loader,  # type: Loader
-              avsc_names,       # type: Names
-              metadata,         # type: Dict[Text, Any]
-              uri,              # type: Text
-              makeTool,         # type: Callable[..., Process]
-              kwargs            # type: dict
+              avsc_names,  # type: Names
+              metadata,  # type: Dict[Text, Any]
+              uri,  # type: Text
+              makeTool,  # type: Callable[..., Process]
+              kwargs  # type: dict
               ):
     # type: (...) -> Process
     """Make a Python CWL object."""
@@ -236,16 +239,17 @@ def make_tool(document_loader,  # type: Loader
 
 
 def load_tool(argsworkflow,  # type: Union[Text, Dict[Text, Any]]
-              makeTool,      # type: Callable[..., Process]
-              kwargs=None,   # type: dict
+              makeTool,  # type: Callable[..., Process]
+              kwargs=None,  # type: dict
               enable_dev=False,  # type: bool
-              strict=True,       # type: bool
-              resolver=None,     # type: Callable[[Loader, Union[Text, dict[Text, Any]]], Text]
+              strict=True,  # type: bool
+              resolver=None,  # type: Callable[[Loader, Union[Text, dict[Text, Any]]], Text]
               fetcher_constructor=None  # type: Callable[[Dict[unicode, unicode], requests.sessions.Session], Fetcher]
               ):
     # type: (...) -> Process
 
-    document_loader, workflowobj, uri = fetch_document(argsworkflow, resolver=resolver, fetcher_constructor=fetcher_constructor)
+    document_loader, workflowobj, uri = fetch_document(argsworkflow, resolver=resolver,
+                                                       fetcher_constructor=fetcher_constructor)
     document_loader, avsc_names, processobj, metadata, uri = validate_document(
         document_loader, workflowobj, uri, enable_dev=enable_dev,
         strict=strict, fetcher_constructor=fetcher_constructor)
diff --git a/cwltool/main.py b/cwltool/main.py
index 35c4f2e27..83dd9f112 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -1,39 +1,33 @@
 #!/usr/bin/env python
 
 import argparse
+import functools
 import json
+import logging
 import os
 import sys
-import logging
-import copy
 import tempfile
-import ruamel.yaml as yaml
-import urlparse
-import hashlib
-import pkg_resources  # part of setuptools
-import functools
 
-import rdflib
+import pkg_resources  # part of setuptools
 import requests
-from typing import (Union, Any, AnyStr, cast, Callable, Dict, Sequence, Text,
-    Tuple, Type, IO)
-
-from schema_salad.ref_resolver import Loader, Fetcher, file_uri, uri_file_path
+import ruamel.yaml as yaml
 import schema_salad.validate as validate
-import schema_salad.jsonld_context
-import schema_salad.makedoc
+from schema_salad.ref_resolver import Loader, Fetcher, file_uri, uri_file_path
 from schema_salad.sourceline import strip_dup_lineno
+from typing import (Union, Any, AnyStr, cast, Callable, Dict, Sequence, Text,
+                    Tuple, IO)
 
+from . import draft2tool
 from . import workflow
-from .errors import WorkflowException, UnsupportedRequirement
+from .builder import adjustFileObjs
+from .pathmapper import adjustDirObjs
 from .cwlrdf import printrdf, printdot
-from .process import shortname, Process, getListing, relocateOutputs, cleanIntermediate, scandeps, normalizeFilesDirs
+from .errors import WorkflowException, UnsupportedRequirement
 from .load_tool import fetch_document, validate_document, make_tool
-from . import draft2tool
+from .pack import pack
+from .process import shortname, Process, getListing, relocateOutputs, cleanIntermediate, scandeps, normalizeFilesDirs
 from .resolver import tool_resolver
-from .builder import adjustFileObjs, adjustDirObjs
 from .stdfsaccess import StdFsAccess
-from .pack import pack
 
 _logger = logging.getLogger("cwltool")
 
@@ -65,12 +59,12 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--rm-container", action="store_true", default=True,
-                        help="Delete Docker container used by jobs after they exit (default)",
-                        dest="rm_container")
+                         help="Delete Docker container used by jobs after they exit (default)",
+                         dest="rm_container")
 
     exgroup.add_argument("--leave-container", action="store_false",
-                        default=True, help="Do not delete Docker container used by jobs after they exit",
-                        dest="rm_container")
+                         default=True, help="Do not delete Docker container used by jobs after they exit",
+                         dest="rm_container")
 
     parser.add_argument("--tmpdir-prefix", type=Text,
                         help="Path prefix for temporary directories",
@@ -78,29 +72,29 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--tmp-outdir-prefix", type=Text,
-                        help="Path prefix for intermediate output directories",
-                        default="tmp")
+                         help="Path prefix for intermediate output directories",
+                         default="tmp")
 
     exgroup.add_argument("--cachedir", type=Text, default="",
-                        help="Directory to cache intermediate workflow outputs to avoid recomputing steps.")
+                         help="Directory to cache intermediate workflow outputs to avoid recomputing steps.")
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--rm-tmpdir", action="store_true", default=True,
-                        help="Delete intermediate temporary directories (default)",
-                        dest="rm_tmpdir")
+                         help="Delete intermediate temporary directories (default)",
+                         dest="rm_tmpdir")
 
     exgroup.add_argument("--leave-tmpdir", action="store_false",
-                        default=True, help="Do not delete intermediate temporary directories",
-                        dest="rm_tmpdir")
+                         default=True, help="Do not delete intermediate temporary directories",
+                         dest="rm_tmpdir")
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--move-outputs", action="store_const", const="move", default="move",
-                        help="Move output files to the workflow output directory and delete intermediate output directories (default).",
-                        dest="move_outputs")
+                         help="Move output files to the workflow output directory and delete intermediate output directories (default).",
+                         dest="move_outputs")
 
     exgroup.add_argument("--leave-outputs", action="store_const", const="leave", default="move",
-                        help="Leave output files in intermediate output directories.",
-                        dest="move_outputs")
+                         help="Leave output files in intermediate output directories.",
+                         dest="move_outputs")
 
     exgroup.add_argument("--copy-outputs", action="store_const", const="copy", default="move",
                          help="Copy output files to the workflow output directory, don't delete intermediate output directories.",
@@ -108,10 +102,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--enable-pull", default=True, action="store_true",
-                        help="Try to pull Docker images", dest="enable_pull")
+                         help="Try to pull Docker images", dest="enable_pull")
 
     exgroup.add_argument("--disable-pull", default=True, action="store_false",
-                        help="Do not try to pull Docker images", dest="enable_pull")
+                         help="Do not try to pull Docker images", dest="enable_pull")
 
     parser.add_argument("--rdf-serializer",
                         help="Output RDF serialization format used by --print-rdf (one of turtle (default), n3, nt, xml)",
@@ -124,8 +118,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--print-rdf", action="store_true",
-                        help="Print corresponding RDF graph for workflow and exit")
-    exgroup.add_argument("--print-dot", action="store_true", help="Print workflow visualization in graphviz format and exit")
+                         help="Print corresponding RDF graph for workflow and exit")
+    exgroup.add_argument("--print-dot", action="store_true",
+                         help="Print workflow visualization in graphviz format and exit")
     exgroup.add_argument("--print-pre", action="store_true", help="Print CWL document after preprocessing.")
     exgroup.add_argument("--print-deps", action="store_true", help="Print CWL document dependencies.")
     exgroup.add_argument("--print-input-deps", action="store_true", help="Print input object document dependencies.")
@@ -134,7 +129,8 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
 
     exgroup = parser.add_mutually_exclusive_group()
-    exgroup.add_argument("--strict", action="store_true", help="Strict validation (unrecognized or out of place fields are error)",
+    exgroup.add_argument("--strict", action="store_true",
+                         help="Strict validation (unrecognized or out of place fields are error)",
                          default=True, dest="strict")
     exgroup.add_argument("--non-strict", action="store_false", help="Lenient validation (ignore unrecognized fields)",
                          default=True, dest="strict")
@@ -147,12 +143,12 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
 
     parser.add_argument("--relative-deps", choices=['primary', 'cwd'],
-        default="primary", help="When using --print-deps, print paths "
-        "relative to primary file or current working directory.")
+                        default="primary", help="When using --print-deps, print paths "
+                                                "relative to primary file or current working directory.")
 
     parser.add_argument("--enable-dev", action="store_true",
                         help="Allow loading and running development versions "
-                        "of CWL spec.", default=False)
+                             "of CWL spec.", default=False)
 
     parser.add_argument("--default-container",
                         help="Specify a default docker container that will be used if the workflow fails to specify one.")
@@ -160,26 +156,26 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Disable passing the current uid to 'docker run --user`")
     parser.add_argument("--disable-net", action="store_true",
                         help="Use docker's default networking for containers;"
-                        " the default is to enable networking.")
+                             " the default is to enable networking.")
     parser.add_argument("--custom-net", type=Text,
                         help="Will be passed to `docker run` as the '--net' "
-                        "parameter. Implies '--enable-net'.")
+                             "parameter. Implies '--enable-net'.")
 
     parser.add_argument("--on-error", type=str,
                         help="Desired workflow behavior when a step fails.  One of 'stop' or 'continue'. "
-                        "Default is 'stop'.", default="stop", choices=("stop", "continue"))
+                             "Default is 'stop'.", default="stop", choices=("stop", "continue"))
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--compute-checksum", action="store_true", default=True,
-                        help="Compute checksum of contents while collecting outputs",
-                        dest="compute_checksum")
+                         help="Compute checksum of contents while collecting outputs",
+                         dest="compute_checksum")
     exgroup.add_argument("--no-compute-checksum", action="store_false",
-                        help="Do not compute checksum of contents while collecting outputs",
-                        dest="compute_checksum")
+                         help="Do not compute checksum of contents while collecting outputs",
+                         dest="compute_checksum")
 
     parser.add_argument("--relax-path-checks", action="store_true",
-            default=False, help="Relax requirements on path names. Currently "
-            "allows spaces.", dest="relax_path_checks")
+                        default=False, help="Relax requirements on path names. Currently "
+                                            "allows spaces.", dest="relax_path_checks")
     parser.add_argument("workflow", type=Text, nargs="?", default=None)
     parser.add_argument("job_order", nargs=argparse.REMAINDER)
 
@@ -200,14 +196,14 @@ def output_callback(out, processStatus):
 
     output_dirs = set()
     finaloutdir = kwargs.get("outdir")
-    kwargs["outdir"] = tempfile.mkdtemp(prefix=kwargs["tmp_outdir_prefix"]) if kwargs.get("tmp_outdir_prefix") else tempfile.mkdtemp()
+    kwargs["outdir"] = tempfile.mkdtemp(prefix=kwargs["tmp_outdir_prefix"]) if kwargs.get(
+        "tmp_outdir_prefix") else tempfile.mkdtemp()
     output_dirs.add(kwargs["outdir"])
 
     jobReqs = None
     if "cwl:requirements" in job_order_object:
         jobReqs = job_order_object["cwl:requirements"]
-    elif ("cwl:defaults" in t.metadata and "cwl:requirements" in
-            t.metadata["cwl:defaults"]):
+    elif ("cwl:defaults" in t.metadata and "cwl:requirements" in t.metadata["cwl:defaults"]):
         jobReqs = t.metadata["cwl:defaults"]["cwl:requirements"]
     if jobReqs:
         for req in jobReqs:
@@ -244,6 +240,7 @@ def output_callback(out, processStatus):
     else:
         return (None, "permanentFail")
 
+
 class FSAction(argparse.Action):
     objclass = None  # type: Text
 
@@ -256,9 +253,10 @@ def __init__(self, option_strings, dest, nargs=None, **kwargs):
     def __call__(self, parser, namespace, values, option_string=None):
         # type: (argparse.ArgumentParser, argparse.Namespace, Union[AnyStr, Sequence[Any], None], AnyStr) -> None
         setattr(namespace,
-            self.dest,  # type: ignore
-            {"class": self.objclass,
-             "location": file_uri(str(os.path.abspath(cast(AnyStr, values))))})
+                self.dest,  # type: ignore
+                {"class": self.objclass,
+                 "location": file_uri(str(os.path.abspath(cast(AnyStr, values))))})
+
 
 class FSAppendAction(argparse.Action):
     objclass = None  # type: Text
@@ -283,90 +281,94 @@ def __call__(self, parser, namespace, values, option_string=None):
             {"class": self.objclass,
              "location": file_uri(str(os.path.abspath(cast(AnyStr, values))))})
 
+
 class FileAction(FSAction):
     objclass = "File"
 
+
 class DirectoryAction(FSAction):
     objclass = "Directory"
 
+
 class FileAppendAction(FSAppendAction):
     objclass = "File"
 
+
 class DirectoryAppendAction(FSAppendAction):
     objclass = "Directory"
 
 
 def add_argument(toolparser, name, inptype, records, description="",
-        default=None):
+                 default=None):
     # type: (argparse.ArgumentParser, Text, Any, List[Text], Text, Any) -> None
-        if len(name) == 1:
-            flag = "-"
-        else:
-            flag = "--"
-
-        required = True
-        if isinstance(inptype, list):
-            if inptype[0] == "null":
-                required = False
-                if len(inptype) == 2:
-                    inptype = inptype[1]
-                else:
-                    _logger.debug(u"Can't make command line argument from %s", inptype)
-                    return None
-
-        ahelp = description.replace("%", "%%")
-        action = None  # type: Union[argparse.Action, Text]
-        atype = None  # type: Any
-
-        if inptype == "File":
-            action = cast(argparse.Action, FileAction)
-        elif inptype == "Directory":
-            action = cast(argparse.Action, DirectoryAction)
-        elif isinstance(inptype, dict) and inptype["type"] == "array":
-            if inptype["items"] == "File":
-                action = cast(argparse.Action, FileAppendAction)
-            elif inptype["items"] == "Directory":
-                action = cast(argparse.Action, DirectoryAppendAction)
-            else:
-                action = "append"
-        elif isinstance(inptype, dict) and inptype["type"] == "enum":
-            atype = Text
-        elif isinstance(inptype, dict) and inptype["type"] == "record":
-            records.append(name)
-            for field in inptype['fields']:
-                fieldname = name+"."+shortname(field['name'])
-                fieldtype = field['type']
-                fielddescription = field.get("doc", "")
-                add_argument(
-                    toolparser, fieldname, fieldtype, records,
-                    fielddescription)
-            return
-        if inptype == "string":
-            atype = Text
-        elif inptype == "int":
-            atype = int
-        elif inptype == "double":
-            atype = float
-        elif inptype == "float":
-            atype = float
-        elif inptype == "boolean":
-            action = "store_true"
-
-        if default:
-            required = False
-
-        if not atype and not action:
-            _logger.debug(u"Can't make command line argument from %s", inptype)
-            return None
+    if len(name) == 1:
+        flag = "-"
+    else:
+        flag = "--"
 
-        if inptype != "boolean":
-            typekw = { 'type': atype }
+    required = True
+    if isinstance(inptype, list):
+        if inptype[0] == "null":
+            required = False
+            if len(inptype) == 2:
+                inptype = inptype[1]
+            else:
+                _logger.debug(u"Can't make command line argument from %s", inptype)
+                return None
+
+    ahelp = description.replace("%", "%%")
+    action = None  # type: Union[argparse.Action, Text]
+    atype = None  # type: Any
+
+    if inptype == "File":
+        action = cast(argparse.Action, FileAction)
+    elif inptype == "Directory":
+        action = cast(argparse.Action, DirectoryAction)
+    elif isinstance(inptype, dict) and inptype["type"] == "array":
+        if inptype["items"] == "File":
+            action = cast(argparse.Action, FileAppendAction)
+        elif inptype["items"] == "Directory":
+            action = cast(argparse.Action, DirectoryAppendAction)
         else:
-            typekw = {}
+            action = "append"
+    elif isinstance(inptype, dict) and inptype["type"] == "enum":
+        atype = Text
+    elif isinstance(inptype, dict) and inptype["type"] == "record":
+        records.append(name)
+        for field in inptype['fields']:
+            fieldname = name + "." + shortname(field['name'])
+            fieldtype = field['type']
+            fielddescription = field.get("doc", "")
+            add_argument(
+                toolparser, fieldname, fieldtype, records,
+                fielddescription)
+        return
+    if inptype == "string":
+        atype = Text
+    elif inptype == "int":
+        atype = int
+    elif inptype == "double":
+        atype = float
+    elif inptype == "float":
+        atype = float
+    elif inptype == "boolean":
+        action = "store_true"
+
+    if default:
+        required = False
+
+    if not atype and not action:
+        _logger.debug(u"Can't make command line argument from %s", inptype)
+        return None
+
+    if inptype != "boolean":
+        typekw = {'type': atype}
+    else:
+        typekw = {}
 
-        toolparser.add_argument(  # type: ignore
-            flag + name, required=required, help=ahelp, action=action,
-            default=default, **typekw)
+    toolparser.add_argument(  # type: ignore
+        flag + name, required=required, help=ahelp, action=action,
+        default=default, **typekw)
 
 
 def generate_parser(toolparser, tool, namemap, records):
@@ -431,16 +433,17 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
             for record_name in records:
                 record = {}
                 record_items = {
-                    k:v for k,v in cmd_line.iteritems()
+                    k: v for k, v in cmd_line.iteritems()
                     if k.startswith(record_name)}
                 for key, value in record_items.iteritems():
-                    record[key[len(record_name)+1:]] = value
+                    record[key[len(record_name) + 1:]] = value
                     del cmd_line[key]
                 cmd_line[str(record_name)] = record
 
             if cmd_line["job_order"]:
                 try:
-                    input_basedir = args.basedir if args.basedir else os.path.abspath(os.path.dirname(cmd_line["job_order"]))
+                    input_basedir = args.basedir if args.basedir else os.path.abspath(
+                        os.path.dirname(cmd_line["job_order"]))
                     job_order_object = loader.resolve_ref(cmd_line["job_order"])
                 except Exception as e:
                     _logger.error(Text(e), exc_info=args.debug)
@@ -448,7 +451,7 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
             else:
                 job_order_object = {"id": args.workflow}
 
-            job_order_object.update({namemap[k]: v for k,v in cmd_line.items()})
+            job_order_object.update({namemap[k]: v for k, v in cmd_line.items()})
 
             if _logger.isEnabledFor(logging.DEBUG):
                 _logger.debug(u"Parsed job order from command line: %s", json.dumps(job_order_object, indent=4))
@@ -471,7 +474,7 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
 
     if print_input_deps:
         printdeps(job_order_object, loader, stdout, relative_deps, "",
-                  basedir=file_uri(input_basedir+"/"))
+                  basedir=file_uri(input_basedir + "/"))
         return 0
 
     def pathToLoc(p):
@@ -483,7 +486,7 @@ def pathToLoc(p):
     adjustFileObjs(job_order_object, pathToLoc)
     normalizeFilesDirs(job_order_object)
     adjustDirObjs(job_order_object, cast(Callable[..., Any],
-        functools.partial(getListing, make_fs_access(input_basedir))))
+                                         functools.partial(getListing, make_fs_access(input_basedir))))
 
     if "cwl:tool" in job_order_object:
         del job_order_object["cwl:tool"]
@@ -492,6 +495,7 @@ def pathToLoc(p):
 
     return (job_order_object, input_basedir)
 
+
 def makeRelative(base, ob):
     u = ob.get("location", ob.get("path"))
     if ":" in u.split("/")[0] and not u.startswith("file://"):
@@ -501,6 +505,7 @@ def makeRelative(base, ob):
             u = uri_file_path(u)
             ob["location"] = os.path.relpath(u, base)
 
+
 def printdeps(obj, document_loader, stdout, relative_deps, uri, basedir=None):
     # type: (Dict[Text, Any], Loader, IO[Any], bool, Text, Text) -> None
     deps = {"class": "File",
@@ -510,8 +515,8 @@ def loadref(b, u):
         return document_loader.fetch(document_loader.fetcher.urljoin(b, u))
 
     sf = scandeps(
-        basedir if basedir else uri, obj, set(("$import", "run")),
-        set(("$include", "$schemas", "location")), loadref)
+        basedir if basedir else uri, obj, {"$import", "run"},
+        {"$include", "$schemas", "location"}, loadref)
     if sf:
         deps["secondaryFiles"] = sf
 
@@ -528,6 +533,7 @@ def loadref(b, u):
 
     stdout.write(json.dumps(deps, indent=4))
 
+
 def print_pack(document_loader, processobj, uri, metadata):
     # type: (Loader, Union[Dict[unicode, Any], List[Dict[unicode, Any]]], unicode, Dict[unicode, Any]) -> str
     packed = pack(document_loader, processobj, uri, metadata)
@@ -536,6 +542,7 @@ def print_pack(document_loader, processobj, uri, metadata):
     else:
         return json.dumps(packed["$graph"][0], indent=4)
 
+
 def versionstring():
     # type: () -> Text
     pkg = pkg_resources.require("cwltool")
@@ -546,7 +553,7 @@ def versionstring():
 
 
 def main(argsl=None,  # type: List[str]
-         args=None,   # type: argparse.Namespace
+         args=None,  # type: argparse.Namespace
          executor=single_job_executor,  # type: Callable[..., Tuple[Dict[Text, Any], Text]]
          makeTool=workflow.defaultMakeTool,  # type: Callable[..., Process]
          selectResources=None,  # type: Callable[[Dict[Text, int]], Dict[Text, int]]
@@ -577,29 +584,29 @@ def main(argsl=None,  # type: List[str]
         # If caller provided custom arguments, it may be not every expected
         # option is set, so fill in no-op defaults to avoid crashing when
         # dereferencing them in args.
-        for k,v in {'print_deps': False,
-                    'print_pre': False,
-                    'print_rdf': False,
-                    'print_dot': False,
-                    'relative_deps': False,
-                    'tmp_outdir_prefix': 'tmp',
-                    'tmpdir_prefix': 'tmp',
-                    'print_input_deps': False,
-                    'cachedir': None,
-                    'quiet': False,
-                    'debug': False,
-                    'version': False,
-                    'enable_dev': False,
-                    'strict': True,
-                    'rdf_serializer': None,
-                    'basedir': None,
-                    'tool_help': False,
-                    'workflow': None,
-                    'job_order': None,
-                    'pack': False,
-                    'on_error': 'continue',
-                    'relax_path_checks': False,
-                    'validate': False}.iteritems():
+        for k, v in {'print_deps': False,
+                     'print_pre': False,
+                     'print_rdf': False,
+                     'print_dot': False,
+                     'relative_deps': False,
+                     'tmp_outdir_prefix': 'tmp',
+                     'tmpdir_prefix': 'tmp',
+                     'print_input_deps': False,
+                     'cachedir': None,
+                     'quiet': False,
+                     'debug': False,
+                     'version': False,
+                     'enable_dev': False,
+                     'strict': True,
+                     'rdf_serializer': None,
+                     'basedir': None,
+                     'tool_help': False,
+                     'workflow': None,
+                     'job_order': None,
+                     'pack': False,
+                     'on_error': 'continue',
+                     'relax_path_checks': False,
+                     'validate': False}.iteritems():
             if not hasattr(args, k):
                 setattr(args, k, v)
 
@@ -625,7 +632,8 @@ def main(argsl=None,  # type: List[str]
             draft2tool.ACCEPTLIST_RE = draft2tool.ACCEPTLIST_EN_RELAXED_RE
 
         try:
-            document_loader, workflowobj, uri = fetch_document(args.workflow, resolver=resolver, fetcher_constructor=fetcher_constructor)
+            document_loader, workflowobj, uri = fetch_document(args.workflow, resolver=resolver,
+                                                               fetcher_constructor=fetcher_constructor)
 
             if args.print_deps:
                 printdeps(workflowobj, document_loader, stdout, args.relative_deps, uri)
@@ -649,7 +657,7 @@ def main(argsl=None,  # type: List[str]
                 return 0
 
             tool = make_tool(document_loader, avsc_names, metadata, uri,
-                    makeTool, vars(args))
+                             makeTool, vars(args))
 
             if args.print_rdf:
                 printrdf(tool, document_loader.ctx, args.rdf_serializer, stdout)
@@ -682,7 +690,7 @@ def main(argsl=None,  # type: List[str]
             if getattr(args, dirprefix) and getattr(args, dirprefix) != 'tmp':
                 sl = "/" if getattr(args, dirprefix).endswith("/") or dirprefix == "cachedir" else ""
                 setattr(args, dirprefix,
-                        os.path.abspath(getattr(args, dirprefix))+sl)
+                        os.path.abspath(getattr(args, dirprefix)) + sl)
                 if not os.path.exists(os.path.dirname(getattr(args, dirprefix))):
                     try:
                         os.makedirs(os.path.dirname(getattr(args, dirprefix)))
@@ -711,10 +719,10 @@ def main(argsl=None,  # type: List[str]
             del args.workflow
             del args.job_order
             (out, status) = executor(tool, job_order_object[0],
-                           makeTool=makeTool,
-                           select_resources=selectResources,
-                           make_fs_access=make_fs_access,
-                           **vars(args))
+                                     makeTool=makeTool,
+                                     select_resources=selectResources,
+                                     make_fs_access=make_fs_access,
+                                     **vars(args))
 
             # This is the workflow output, it needs to be written
             if out is not None:
@@ -741,7 +749,7 @@ def locToPath(p):
 
         except (validate.ValidationException) as exc:
             _logger.error(u"Input object failed validation:\n%s", exc,
-                    exc_info=args.debug)
+                          exc_info=args.debug)
             return 1
         except UnsupportedRequirement as exc:
             _logger.error(
@@ -759,7 +767,6 @@ def locToPath(p):
                 "  %s", exc, exc_info=args.debug)
             return 1
 
-        return 0
     finally:
         _logger.removeHandler(stderr_handler)
         _logger.addHandler(defaultStreamHandler)
diff --git a/cwltool/pack.py b/cwltool/pack.py
index 6d41f6e00..30f95cdea 100644
--- a/cwltool/pack.py
+++ b/cwltool/pack.py
@@ -2,10 +2,10 @@
 import urlparse
 
 from schema_salad.ref_resolver import Loader
+from typing import Union, Any, cast, Callable, Dict, Text
 
-from .process import scandeps, shortname, uniquename
+from .process import shortname, uniquename
 
-from typing import Union, Any, cast, Callable, Dict, Tuple, Type, IO, Text
 
 def flatten_deps(d, files):  # type: (Any, Set[Text]) -> None
     if isinstance(d, list):
@@ -19,6 +19,7 @@ def flatten_deps(d, files):  # type: (Any, Set[Text]) -> None
         if "listing" in d:
             flatten_deps(d["listing"], files)
 
+
 def find_run(d, loadref, runs):  # type: (Any, Callable[[Text, Text], Union[Dict, List, Text]], Set[Text]) -> None
     if isinstance(d, list):
         for s in d:
@@ -31,6 +32,7 @@ def find_run(d, loadref, runs):  # type: (Any, Callable[[Text, Text], Union[Dict
         for s in d.values():
             find_run(s, loadref, runs)
 
+
 def find_ids(d, ids):  # type: (Any, Set[Text]) -> None
     if isinstance(d, list):
         for s in d:
@@ -42,10 +44,11 @@ def find_ids(d, ids):  # type: (Any, Set[Text]) -> None
         for s in d.values():
             find_ids(s, ids)
 
+
 def replace_refs(d, rewrite, stem, newstem):
     # type: (Any, Dict[Text, Text], Text, Text) -> None
     if isinstance(d, list):
-        for s,v in enumerate(d):
+        for s, v in enumerate(d):
             if isinstance(v, (str, unicode)):
                 if v in rewrite:
                     d[s] = rewrite[v]
@@ -54,7 +57,7 @@ def replace_refs(d, rewrite, stem, newstem):
             else:
                 replace_refs(v, rewrite, stem, newstem)
     elif isinstance(d, dict):
-        for s,v in d.items():
+        for s, v in d.items():
             if isinstance(v, (str, unicode)):
                 if v in rewrite:
                     d[s] = rewrite[v]
@@ -62,13 +65,14 @@ def replace_refs(d, rewrite, stem, newstem):
                     d[s] = newstem + v[len(stem):]
             replace_refs(v, rewrite, stem, newstem)
 
+
 def pack(document_loader, processobj, uri, metadata):
     # type: (Loader, Union[Dict[Text, Any], List[Dict[Text, Any]]], Text, Dict[Text, Text]) -> Dict[Text, Any]
     def loadref(b, u):
         # type: (Text, Text) -> Union[Dict, List, Text]
         return document_loader.resolve_ref(u, base_url=b)[0]
 
-    runs = set((uri,))
+    runs = {uri}
     find_run(processobj, loadref, runs)
 
     ids = set()  # type: Set[Text]
@@ -76,7 +80,7 @@ def loadref(b, u):
         find_ids(document_loader.resolve_ref(f)[0], ids)
 
     names = set()  # type: Set[Text]
-    rewrite = {}   # type: Dict[Text, Text]
+    rewrite = {}  # type: Dict[Text, Text]
 
     mainpath, _ = urlparse.urldefrag(uri)
 
@@ -101,7 +105,7 @@ def rewrite_id(r, mainuri):
             rewrite_id(r, uri)
 
     packed = {"$graph": [], "cwlVersion": metadata["cwlVersion"]
-            }  # type: Dict[Text, Any]
+              }  # type: Dict[Text, Any]
 
     schemas = set()  # type: Set[Text]
     for r in sorted(runs):
@@ -127,6 +131,6 @@ def rewrite_id(r, mainuri):
 
     for r in rewrite:
         v = rewrite[r]
-        replace_refs(packed, rewrite, r+"/" if "#" in r else r+"#", v+"/")
+        replace_refs(packed, rewrite, r + "/" if "#" in r else r + "#", v + "/")
 
     return packed
diff --git a/cwltool/pathmapper.py b/cwltool/pathmapper.py
index 3e1aa2e3f..2bdfbc517 100644
--- a/cwltool/pathmapper.py
+++ b/cwltool/pathmapper.py
@@ -1,20 +1,22 @@
-import os
+import collections
 import logging
+import os
 import stat
-import collections
-import uuid
 import urllib
 import urlparse
+import uuid
 from functools import partial
-from typing import Any, Callable, Set, Text, Tuple, Union
+
 import schema_salad.validate as validate
-from schema_salad.sourceline import SourceLine
 from schema_salad.ref_resolver import uri_file_path
+from schema_salad.sourceline import SourceLine
+from typing import Any, Callable, Set, Text, Tuple, Union
 
 _logger = logging.getLogger("cwltool")
 
 MapperEnt = collections.namedtuple("MapperEnt", ["resolved", "target", "type"])
 
+
 def adjustFiles(rec, op):  # type: (Any, Union[Callable[..., Any], partial[Any]]) -> None
     """Apply a mapping function to each File path in the object `rec`."""
 
@@ -27,6 +29,7 @@ def adjustFiles(rec, op):  # type: (Any, Union[Callable[..., Any], partial[Any]]
         for d in rec:
             adjustFiles(d, op)
 
+
 def adjustFileObjs(rec, op):  # type: (Any, Union[Callable[..., Any], partial[Any]]) -> None
     """Apply an update function to each File object in the object `rec`."""
 
@@ -39,6 +42,7 @@ def adjustFileObjs(rec, op):  # type: (Any, Union[Callable[..., Any], partial[An
         for d in rec:
             adjustFileObjs(d, op)
 
+
 def adjustDirObjs(rec, op):
     # type: (Any, Union[Callable[..., Any], partial[Any]]) -> None
     """Apply an update function to each Directory object in the object `rec`."""
@@ -52,6 +56,7 @@ def adjustDirObjs(rec, op):
         for d in rec:
             adjustDirObjs(d, op)
 
+
 def normalizeFilesDirs(job):
     # type: (Union[List[Dict[Text, Any]], Dict[Text, Any]]) -> None
     def addLocation(d):
@@ -59,7 +64,8 @@ def addLocation(d):
             if d["class"] == "File" and ("contents" not in d):
                 raise validate.ValidationException("Anonymous file object must have 'contents' and 'basename' fields.")
             if d["class"] == "Directory" and ("listing" not in d or "basename" not in d):
-                raise validate.ValidationException("Anonymous directory object must have 'listing' and 'basename' fields.")
+                raise validate.ValidationException(
+                    "Anonymous directory object must have 'listing' and 'basename' fields.")
             d["location"] = "_:" + Text(uuid.uuid4())
             if "basename" not in d:
                 d["basename"] = Text(uuid.uuid4())
@@ -79,6 +85,7 @@ def abspath(src, basedir):  # type: (Text, Text) -> Text
         ab = src if os.path.isabs(src) else os.path.join(basedir, src)
     return ab
 
+
 def dedup(listing):  # type: (List[Any]) -> List[Any]
     marksub = set()
 
@@ -102,7 +109,6 @@ def mark(d):
 
 
 class PathMapper(object):
-
     """Mapping of files from relative path provided in the file to a tuple of
     (absolute local path, absolute container path)
 
diff --git a/cwltool/process.py b/cwltool/process.py
index ca0b19550..92f3903d8 100644
--- a/cwltool/process.py
+++ b/cwltool/process.py
@@ -1,39 +1,36 @@
-import os
-import json
+import abc
 import copy
+import errno
+import hashlib
+import json
 import logging
-import pprint
+import os
+import shutil
 import stat
 import tempfile
-import glob
 import urlparse
-from collections import Iterable
-import errno
-import shutil
 import uuid
-import hashlib
+from collections import Iterable
 
-import abc
-import schema_salad.validate as validate
-import schema_salad.schema
-from schema_salad.ref_resolver import Loader, file_uri
-from schema_salad.sourceline import SourceLine
 import avro.schema
-from typing import (Any, AnyStr, Callable, cast, Dict, List, Generator, IO, Text,
-        Tuple, Union)
+import schema_salad.schema
+import schema_salad.validate as validate
+from pkg_resources import resource_stream
+from rdflib import Graph
 from rdflib import URIRef
 from rdflib.namespace import RDFS, OWL
-from rdflib import Graph
-from pkg_resources import resource_stream
-
-
 from ruamel.yaml.comments import CommentedSeq, CommentedMap
+from schema_salad.ref_resolver import Loader, file_uri
+from schema_salad.sourceline import SourceLine
+from typing import (Any, AnyStr, Callable, cast, Dict, List, Generator, Text,
+                    Tuple, Union)
 
-from .utils import aslist, get_feature
-from .stdfsaccess import StdFsAccess
-from .builder import Builder, adjustFileObjs, adjustDirObjs
+from .builder import Builder, adjustFileObjs
+from .pathmapper import adjustDirObjs
 from .errors import WorkflowException, UnsupportedRequirement
-from .pathmapper import PathMapper, abspath, normalizeFilesDirs
+from .pathmapper import PathMapper, normalizeFilesDirs
+from .stdfsaccess import StdFsAccess
+from .utils import aslist, get_feature
 
 _logger = logging.getLogger("cwltool")
 
@@ -61,31 +58,32 @@
 
 salad_files = ('metaschema.yml',
                'metaschema_base.yml',
-              'salad.md',
-              'field_name.yml',
-              'import_include.md',
-              'link_res.yml',
-              'ident_res.yml',
-              'vocab_res.yml',
-              'vocab_res.yml',
-              'field_name_schema.yml',
-              'field_name_src.yml',
-              'field_name_proc.yml',
-              'ident_res_schema.yml',
-              'ident_res_src.yml',
-              'ident_res_proc.yml',
-              'link_res_schema.yml',
-              'link_res_src.yml',
-              'link_res_proc.yml',
-              'vocab_res_schema.yml',
-              'vocab_res_src.yml',
-              'vocab_res_proc.yml')
+               'salad.md',
+               'field_name.yml',
+               'import_include.md',
+               'link_res.yml',
+               'ident_res.yml',
+               'vocab_res.yml',
+               'vocab_res.yml',
+               'field_name_schema.yml',
+               'field_name_src.yml',
+               'field_name_proc.yml',
+               'ident_res_schema.yml',
+               'ident_res_src.yml',
+               'ident_res_proc.yml',
+               'link_res_schema.yml',
+               'link_res_src.yml',
+               'link_res_proc.yml',
+               'vocab_res_schema.yml',
+               'vocab_res_src.yml',
+               'vocab_res_proc.yml')
 
 SCHEMA_CACHE = {}  # type: Dict[Text, Tuple[Loader, Union[avro.schema.Names, avro.schema.SchemaParseException], Dict[Text, Any], Loader]]
 SCHEMA_FILE = None  # type: Dict[Text, Any]
 SCHEMA_DIR = None  # type: Dict[Text, Any]
 SCHEMA_ANY = None  # type: Dict[Text, Any]
 
+
 def get_schema(version):
     # type: (Text) -> Tuple[Loader, Union[avro.schema.Names, avro.schema.SchemaParseException], Dict[Text,Any], Loader]
 
@@ -108,7 +106,7 @@ def get_schema(version):
         try:
             res = resource_stream(
                 __name__, 'schemas/%s/salad/schema_salad/metaschema/%s'
-                % (version, f))
+                          % (version, f))
             cache["https://w3id.org/cwl/salad/schema_salad/metaschema/"
                   + f] = res.read()
             res.close()
@@ -120,6 +118,7 @@ def get_schema(version):
 
     return SCHEMA_CACHE[version]
 
+
 def shortname(inputid):
     # type: (Text) -> Text
     d = urlparse.urlparse(inputid)
@@ -128,6 +127,7 @@ def shortname(inputid):
     else:
         return d.path.split(u"/")[-1]
 
+
 def checkRequirements(rec, supportedProcessRequirements):
     # type: (Any, Iterable[Any]) -> None
     if isinstance(rec, dict):
@@ -142,6 +142,7 @@ def checkRequirements(rec, supportedProcessRequirements):
         for d in rec:
             checkRequirements(d, supportedProcessRequirements)
 
+
 def adjustFilesWithSecondary(rec, op, primary=None):
     """Apply a mapping function to each File path in the object `rec`, propagating
     the primary file associated with a group of secondary files.
@@ -159,6 +160,7 @@ def adjustFilesWithSecondary(rec, op, primary=None):
         for d in rec:
             adjustFilesWithSecondary(d, op, primary)
 
+
 def getListing(fs_access, rec):
     # type: (StdFsAccess, Dict[Text, Any]) -> None
     if "listing" not in rec:
@@ -174,6 +176,7 @@ def getListing(fs_access, rec):
                 listing.append({"class": "File", "location": ld})
         rec["listing"] = listing
 
+
 def stageFiles(pm, stageFunc, ignoreWritable=False):
     # type: (PathMapper, Callable[..., Any], bool) -> None
     for f, p in pm.items():
@@ -187,6 +190,7 @@ def stageFiles(pm, stageFunc, ignoreWritable=False):
             with open(p.target, "w") as n:
                 n.write(p.resolved.encode("utf-8"))
 
+
 def collectFilesAndDirs(obj, out):
     # type: (Union[Dict[Text, Any], List[Dict[Text, Any]]], List[Dict[Text, Any]]) -> None
     if isinstance(obj, dict):
@@ -199,6 +203,7 @@ def collectFilesAndDirs(obj, out):
         for l in obj:
             collectFilesAndDirs(l, out)
 
+
 def relocateOutputs(outputObj, outdir, output_dirs, action):
     # type: (Union[Dict[Text, Any], List[Dict[Text, Any]]], Text, Set[Text], Text) -> Union[Dict[Text, Any], List[Dict[Text, Any]]]
     if action not in ("move", "copy"):
@@ -232,6 +237,7 @@ def _check_adjust(f):
 
     return outputObj
 
+
 def cleanIntermediate(output_dirs):  # type: (Set[Text]) -> None
     for a in output_dirs:
         if os.path.exists(a) and empty_subtree(a):
@@ -256,17 +262,17 @@ def formatSubclassOf(fmt, cls, ontology, visited):
 
     uriRefFmt = URIRef(fmt)
 
-    for s,p,o in ontology.triples( (uriRefFmt, RDFS.subClassOf, None) ):
+    for s, p, o in ontology.triples((uriRefFmt, RDFS.subClassOf, None)):
         # Find parent classes of `fmt` and search upward
         if formatSubclassOf(o, cls, ontology, visited):
             return True
 
-    for s,p,o in ontology.triples( (uriRefFmt, OWL.equivalentClass, None) ):
+    for s, p, o in ontology.triples((uriRefFmt, OWL.equivalentClass, None)):
         # Find equivalent classes of `fmt` and search horizontally
         if formatSubclassOf(o, cls, ontology, visited):
             return True
 
-    for s,p,o in ontology.triples( (None, OWL.equivalentClass, uriRefFmt) ):
+    for s, p, o in ontology.triples((None, OWL.equivalentClass, uriRefFmt)):
         # Find equivalent classes of `fmt` and search horizontally
         if formatSubclassOf(s, cls, ontology, visited):
             return True
@@ -282,7 +288,9 @@ def checkFormat(actualFile, inputFormats, ontology):
         for inpf in aslist(inputFormats):
             if af["format"] == inpf or formatSubclassOf(af["format"], inpf, ontology, set()):
                 return
-        raise validate.ValidationException(u"Incompatible file format %s required format(s) %s" % (af["format"], inputFormats))
+        raise validate.ValidationException(
+            u"Incompatible file format %s required format(s) %s" % (af["format"], inputFormats))
+
 
 def fillInDefaults(inputs, job):
     # type: (List[Dict[Text, Text]], Dict[Text, Union[Dict[Text, Any], List, Text]]) -> None
@@ -309,13 +317,14 @@ def avroize_type(field_type, name_prefix=""):
     elif isinstance(field_type, dict):
         if field_type["type"] in ("enum", "record"):
             if "name" not in field_type:
-                field_type["name"] = name_prefix+Text(uuid.uuid4())
+                field_type["name"] = name_prefix + Text(uuid.uuid4())
         if field_type["type"] == "record":
             avroize_type(field_type["fields"], name_prefix)
         if field_type["type"] == "array":
             avroize_type(field_type["items"], name_prefix)
     return field_type
 
+
 class Process(object):
     __metaclass__ = abc.ABCMeta
 
@@ -339,9 +348,9 @@ def __init__(self, toolpath_object, **kwargs):
         if SCHEMA_FILE is None:
             get_schema("v1.0")
             SCHEMA_ANY = cast(Dict[Text, Any],
-                    SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/salad#Any"])
+                              SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/salad#Any"])
             SCHEMA_FILE = cast(Dict[Text, Any],
-                    SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#File"])
+                               SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#File"])
             SCHEMA_DIR = cast(Dict[Text, Any],
                               SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#Directory"])
 
@@ -363,7 +372,7 @@ def __init__(self, toolpath_object, **kwargs):
 
         checkRequirements(self.tool, supportedProcessRequirements)
         self.validate_hints(kwargs["avsc_names"], self.tool.get("hints", []),
-                strict=kwargs.get("strict"))
+                            strict=kwargs.get("strict"))
 
         self.schemaDefs = {}  # type: Dict[Text,Dict[Text, Any]]
 
@@ -407,14 +416,17 @@ def __init__(self, toolpath_object, **kwargs):
             self.inputs_record_schema = schema_salad.schema.make_valid_avro(self.inputs_record_schema, {}, set())
             avro.schema.make_avsc_object(self.inputs_record_schema, self.names)
         except avro.schema.SchemaParseException as e:
-            raise validate.ValidationException(u"Got error `%s` while processing inputs of %s:\n%s" % (Text(e), self.tool["id"], json.dumps(self.inputs_record_schema, indent=4)))
+            raise validate.ValidationException(u"Got error `%s` while processing inputs of %s:\n%s" %
+                                               (Text(e), self.tool["id"],
+                                                json.dumps(self.inputs_record_schema, indent=4)))
 
         try:
             self.outputs_record_schema = schema_salad.schema.make_valid_avro(self.outputs_record_schema, {}, set())
             avro.schema.make_avsc_object(self.outputs_record_schema, self.names)
         except avro.schema.SchemaParseException as e:
-            raise validate.ValidationException(u"Got error `%s` while processing outputs of %s:\n%s" % (Text(e), self.tool["id"], json.dumps(self.outputs_record_schema, indent=4)))
-
+            raise validate.ValidationException(u"Got error `%s` while processing outputs of %s:\n%s" %
+                                               (Text(e), self.tool["id"],
+                                                json.dumps(self.outputs_record_schema, indent=4)))
 
     def _init_job(self, joborder, **kwargs):
         # type: (Dict[Text, Text], **Any) -> Builder
@@ -436,7 +448,7 @@ def _init_job(self, joborder, **kwargs):
 
         builder = Builder()
         builder.job = cast(Dict[Text, Union[Dict[Text, Any], List,
-            Text]], copy.deepcopy(joborder))
+                                            Text]], copy.deepcopy(joborder))
 
         # Validate job order
         try:
@@ -459,13 +471,15 @@ def _init_job(self, joborder, **kwargs):
         dockerReq, is_req = self.get_requirement("DockerRequirement")
 
         if dockerReq and is_req and not kwargs.get("use_container"):
-            raise WorkflowException("Document has DockerRequirement under 'requirements' but use_container is false.  DockerRequirement must be under 'hints' or use_container must be true.")
+            raise WorkflowException(
+                "Document has DockerRequirement under 'requirements' but use_container is false.  DockerRequirement must be under 'hints' or use_container must be true.")
 
         builder.make_fs_access = kwargs.get("make_fs_access") or StdFsAccess
         builder.fs_access = builder.make_fs_access(kwargs["basedir"])
 
         if dockerReq and kwargs.get("use_container"):
-            builder.outdir = builder.fs_access.realpath(dockerReq.get("dockerOutputDirectory") or kwargs.get("docker_outdir") or "/var/spool/cwl")
+            builder.outdir = builder.fs_access.realpath(
+                dockerReq.get("dockerOutputDirectory") or kwargs.get("docker_outdir") or "/var/spool/cwl")
             builder.tmpdir = builder.fs_access.realpath(kwargs.get("docker_tmpdir") or "/tmp")
             builder.stagedir = builder.fs_access.realpath(kwargs.get("docker_stagedir") or "/var/lib/cwl")
         else:
@@ -541,18 +555,18 @@ def evalResources(self, builder, kwargs):
         for a in ("cores", "ram", "tmpdir", "outdir"):
             mn = None
             mx = None
-            if resourceReq.get(a+"Min"):
-                mn = builder.do_eval(resourceReq[a+"Min"])
-            if resourceReq.get(a+"Max"):
-                mx = builder.do_eval(resourceReq[a+"Max"])
+            if resourceReq.get(a + "Min"):
+                mn = builder.do_eval(resourceReq[a + "Min"])
+            if resourceReq.get(a + "Max"):
+                mx = builder.do_eval(resourceReq[a + "Max"])
             if mn is None:
                 mn = mx
             elif mx is None:
                 mx = mn
 
             if mn:
-                request[a+"Min"] = mn
-                request[a+"Max"] = mx
+                request[a + "Min"] = mn
+                request[a + "Max"] = mx
 
         if kwargs.get("select_resources"):
             return kwargs["select_resources"](request)
@@ -570,8 +584,8 @@ def validate_hints(self, avsc_names, hints, strict):
             sl = SourceLine(hints, i, validate.ValidationException)
             with sl:
                 if avsc_names.get_name(r["class"], "") is not None:
-                    plain_hint = dict((key,r[key]) for key in r if key not in
-                            self.doc_loader.identifiers)  # strip identifiers
+                    plain_hint = dict((key, r[key]) for key in r if key not in
+                                      self.doc_loader.identifiers)  # strip identifiers
                     validate.validate_ex(
                         avsc_names.get_name(plain_hint["class"], ""),
                         plain_hint, strict=strict)
@@ -589,6 +603,7 @@ def job(self, job_order, output_callbacks, **kwargs):
         # type: (Dict[Text, Text], Callable[[Any, Any], Any], **Any) -> Generator[Any, None, None]
         return None
 
+
 def empty_subtree(dirpath):  # type: (Text) -> bool
     # Test if a directory tree contains any files (does not count empty
     # subdirectories)
@@ -610,6 +625,7 @@ def empty_subtree(dirpath):  # type: (Text) -> bool
 
 _names = set()  # type: Set[Text]
 
+
 def uniquename(stem, names=None):  # type: (Text, Set[Text]) -> Text
     global _names
     if names is None:
@@ -622,6 +638,7 @@ def uniquename(stem, names=None):  # type: (Text, Set[Text]) -> Text
     names.add(u)
     return u
 
+
 def nestdir(base, deps):
     # type: (Text, Dict[Text, Any]) -> Dict[Text, Any]
     dirname = os.path.dirname(base) + "/"
@@ -639,6 +656,7 @@ def nestdir(base, deps):
             }
     return deps
 
+
 def mergedirs(listing):
     # type: (List[Dict[Text, Any]]) -> List[Dict[Text, Any]]
     r = []  # type: List[Dict[Text, Any]]
@@ -654,6 +672,7 @@ def mergedirs(listing):
     r.extend(ents.itervalues())
     return r
 
+
 def scandeps(base, doc, reffields, urlfields, loadref, urljoin=urlparse.urljoin):
     # type: (Text, Any, Set[Text], Set[Text], Callable[[Text, Text], Any], Callable[[Text, Text], Text]) -> List[Dict[Text, Text]]
     r = []  # type: List[Dict[Text, Text]]
@@ -725,14 +744,15 @@ def scandeps(base, doc, reffields, urlfields, loadref, urljoin=urlparse.urljoin)
 
     return r
 
+
 def compute_checksums(fs_access, fileobj):
     if "checksum" not in fileobj:
         checksum = hashlib.sha1()
         with fs_access.open(fileobj["location"], "rb") as f:
-            contents = f.read(1024*1024)
+            contents = f.read(1024 * 1024)
             while contents != "":
                 checksum.update(contents)
-                contents = f.read(1024*1024)
+                contents = f.read(1024 * 1024)
             f.seek(0, 2)
             filesize = f.tell()
         fileobj["checksum"] = "sha1$%s" % checksum.hexdigest()
diff --git a/cwltool/resolver.py b/cwltool/resolver.py
index cf753f362..8a08fbba3 100644
--- a/cwltool/resolver.py
+++ b/cwltool/resolver.py
@@ -1,12 +1,11 @@
-import os
 import logging
-import urllib
-import urlparse
+import os
 
 from schema_salad.ref_resolver import file_uri
 
 _logger = logging.getLogger("cwltool")
 
+
 def resolve_local(document_loader, uri):
     if uri.startswith("/"):
         return None
@@ -24,6 +23,7 @@ def resolve_local(document_loader, uri):
             return file_uri(s)
     return None
 
+
 def tool_resolver(document_loader, uri):
     for r in [resolve_local]:
         ret = r(document_loader, uri)
diff --git a/cwltool/sandboxjs.py b/cwltool/sandboxjs.py
index 70a9f1976..21c3a532f 100644
--- a/cwltool/sandboxjs.py
+++ b/cwltool/sandboxjs.py
@@ -1,15 +1,16 @@
-import subprocess
-import json
-import threading
+import cStringIO
 import errno
+import json
 import logging
-import select
 import os
-
-import cStringIO
+import select
+import subprocess
+import threading
 from cStringIO import StringIO
-from typing import Any, Dict, List, Mapping, Text, TypeVar, Union
+
 from pkg_resources import resource_stream
+from typing import Any, Dict, List, Mapping, Text, Union
+
 
 class JavascriptException(Exception):
     pass
@@ -17,12 +18,13 @@ class JavascriptException(Exception):
 
 _logger = logging.getLogger("cwltool")
 
-JSON = Union[Dict[Text,Any], List[Any], Text, int, long, float, bool, None]
+JSON = Union[Dict[Text, Any], List[Any], Text, int, long, float, bool, None]
 
 localdata = threading.local()
 
 have_node_slim = False
 
+
 def new_js_proc():
     # type: () -> subprocess.Popen
 
@@ -33,7 +35,8 @@ def new_js_proc():
     trynodes = ("nodejs", "node")
     for n in trynodes:
         try:
-            nodejs = subprocess.Popen([n, "--eval", nodecode], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            nodejs = subprocess.Popen([n, "--eval", nodecode], stdin=subprocess.PIPE, stdout=subprocess.PIPE,
+                                      stderr=subprocess.PIPE)
             break
         except OSError as e:
             if e.errno == errno.ENOENT:
@@ -80,7 +83,8 @@ def execjs(js, jslib, timeout=None, debug=False):  # type: (Union[Mapping, Text]
 
     nodejs = localdata.proc
 
-    fn = u"\"use strict\";\n%s\n(function()%s)()" % (jslib, js if isinstance(js, basestring) and len(js) > 1 and js[0] == '{' else ("{return (%s);}" % js))
+    fn = u"\"use strict\";\n%s\n(function()%s)()" %\
+         (jslib, js if isinstance(js, basestring) and len(js) > 1 and js[0] == '{' else ("{return (%s);}" % js))
 
     killed = []
 
@@ -97,7 +101,7 @@ def term():
     tm = threading.Timer(timeout, term)
     tm.start()
 
-    stdin_buf = StringIO(json.dumps(fn)+"\n")
+    stdin_buf = StringIO(json.dumps(fn) + "\n")
     stdout_buf = StringIO()
     stderr_buf = StringIO()
 
@@ -132,9 +136,9 @@ def fn_linenum():  # type: () -> Text
         ofs = 0
         maxlines = 99
         if len(lines) > maxlines:
-            ofs = len(lines)-maxlines
+            ofs = len(lines) - maxlines
             lines = lines[-maxlines:]
-        return u"\n".join(u"%02i %s" % (i+ofs+1, b) for i, b in enumerate(lines))
+        return u"\n".join(u"%02i %s" % (i + ofs + 1, b) for i, b in enumerate(lines))
 
     def stdfmt(data):  # type: (unicode) -> unicode
         if "\n" in data:
@@ -142,7 +146,8 @@ def stdfmt(data):  # type: (unicode) -> unicode
         return data
 
     if debug:
-        info = u"returncode was: %s\nscript was:\n%s\nstdout was: %s\nstderr was: %s\n" % (nodejs.returncode, fn_linenum(), stdfmt(stdoutdata), stdfmt(stderrdata))
+        info = u"returncode was: %s\nscript was:\n%s\nstdout was: %s\nstderr was: %s\n" %\
+               (nodejs.returncode, fn_linenum(), stdfmt(stdoutdata), stdfmt(stderrdata))
     else:
         info = stdfmt(stderrdata)
 
@@ -155,4 +160,5 @@ def stdfmt(data):  # type: (unicode) -> unicode
         try:
             return json.loads(stdoutdata)
         except ValueError as e:
-            raise JavascriptException(u"%s\nscript was:\n%s\nstdout was: '%s'\nstderr was: '%s'\n" % (e, fn_linenum(), stdoutdata, stderrdata))
+            raise JavascriptException(u"%s\nscript was:\n%s\nstdout was: '%s'\nstderr was: '%s'\n" %
+                                      (e, fn_linenum(), stdoutdata, stderrdata))
diff --git a/cwltool/stdfsaccess.py b/cwltool/stdfsaccess.py
index 2db2a5dfa..302235ea6 100644
--- a/cwltool/stdfsaccess.py
+++ b/cwltool/stdfsaccess.py
@@ -1,11 +1,13 @@
-from typing import Any, BinaryIO, Text
-from .pathmapper import abspath
 import glob
 import os
+
 from schema_salad.ref_resolver import file_uri
+from typing import BinaryIO, Text
+
+from .pathmapper import abspath
 
-class StdFsAccess(object):
 
+class StdFsAccess(object):
     def __init__(self, basedir):  # type: (Text) -> None
         self.basedir = basedir
 
diff --git a/cwltool/update.py b/cwltool/update.py
index 762ad0317..f549d1a65 100644
--- a/cwltool/update.py
+++ b/cwltool/update.py
@@ -1,18 +1,17 @@
-import sys
-import urlparse
+import copy
 import json
 import re
 import traceback
-import copy
+import urlparse
 
-from schema_salad.ref_resolver import Loader
 import schema_salad.validate
-from typing import Any, Callable, Dict, List, Text, Tuple, Union  # pylint: disable=unused-import
-
 from ruamel.yaml.comments import CommentedSeq, CommentedMap
+from schema_salad.ref_resolver import Loader
+from typing import Any, Callable, Dict, Text, Tuple, Union  # pylint: disable=unused-import
 
 from .utils import aslist
 
+
 def findId(doc, frg):  # type: (Any, Any) -> Dict
     if isinstance(doc, dict):
         if "id" in doc and doc["id"] == frg:
@@ -29,6 +28,7 @@ def findId(doc, frg):  # type: (Any, Any) -> Dict
                 return f
     return None
 
+
 def fixType(doc):  # type: (Any) -> Any
     if isinstance(doc, list):
         for i, f in enumerate(doc):
@@ -42,6 +42,7 @@ def fixType(doc):  # type: (Any) -> Any
             return "#" + doc
     return doc
 
+
 def _draft2toDraft3dev1(doc, loader, baseuri, update_steps=True):
     # type: (Any, Loader, Text, bool) -> Any
     try:
@@ -82,7 +83,6 @@ def _draft2toDraft3dev1(doc, loader, baseuri, update_steps=True):
                                 doc["requirements"] = []
                             doc["requirements"].append({"class": "MultipleInputFeatureRequirement"})
 
-
             for a in doc:
                 doc[a] = _draft2toDraft3dev1(doc[a], loader, baseuri)
 
@@ -99,6 +99,7 @@ def _draft2toDraft3dev1(doc, loader, baseuri, update_steps=True):
             err = doc["name"]
         raise Exception(u"Error updating '%s'\n  %s\n%s" % (err, e, traceback.format_exc()))
 
+
 def draft2toDraft3dev1(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     return (_draft2toDraft3dev1(doc, loader, baseuri), "draft-3.dev1")
@@ -106,6 +107,7 @@ def draft2toDraft3dev1(doc, loader, baseuri):
 
 digits = re.compile("\d+")
 
+
 def updateScript(sc):  # type: (Text) -> Text
     sc = sc.replace("$job", "inputs")
     sc = sc.replace("$tmpdir", "runtime.tmpdir")
@@ -124,7 +126,7 @@ def _updateDev2Script(ent):  # type: (Any) -> Any
                 if not sp[0]:
                     sp.pop(0)
                 front = sp.pop(0)
-                sp = [Text(i) if digits.match(i) else "'"+i+"'"
+                sp = [Text(i) if digits.match(i) else "'" + i + "'"
                       for i in sp]
                 if front == "job":
                     return u"$(inputs[%s])" % ']['.join(sp)
@@ -167,7 +169,7 @@ def _draftDraft3dev1toDev2(doc, loader, baseuri):
                     if r["class"] == "ExpressionEngineRequirement":
                         if "engineConfig" in r:
                             doc["requirements"].append({
-                                "class":"InlineJavascriptRequirement",
+                                "class": "InlineJavascriptRequirement",
                                 "expressionLib": [updateScript(sc) for sc in aslist(r["engineConfig"])]
                             })
                             added = True
@@ -179,7 +181,7 @@ def _draftDraft3dev1toDev2(doc, loader, baseuri):
             else:
                 doc["requirements"] = []
             if not added:
-                doc["requirements"].append({"class":"InlineJavascriptRequirement"})
+                doc["requirements"].append({"class": "InlineJavascriptRequirement"})
 
     elif isinstance(doc, list):
         for i, a in enumerate(doc):
@@ -192,6 +194,7 @@ def draftDraft3dev1toDev2(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     return (_draftDraft3dev1toDev2(doc, loader, baseuri), "draft-3.dev2")
 
+
 def _draftDraft3dev2toDev3(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Any
     try:
@@ -236,6 +239,7 @@ def _draftDraft3dev2toDev3(doc, loader, baseuri):
         import traceback
         raise Exception(u"Error updating '%s'\n  %s\n%s" % (err, e, traceback.format_exc()))
 
+
 def draftDraft3dev2toDev3(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     return (_draftDraft3dev2toDev3(doc, loader, baseuri), "draft-3.dev3")
@@ -298,6 +302,7 @@ def draftDraft3dev3toDev4(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     return (_draftDraft3dev3toDev4(doc, loader, baseuri), "draft-3.dev4")
 
+
 def _draftDraft3dev4toDev5(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Any
     try:
@@ -332,10 +337,12 @@ def draftDraft3dev4toDev5(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     return (_draftDraft3dev4toDev5(doc, loader, baseuri), "draft-3.dev5")
 
+
 def draftDraft3dev5toFinal(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     return (doc, "draft-3")
 
+
 def _draft3toDraft4dev1(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Any
     if isinstance(doc, dict):
@@ -369,11 +376,13 @@ def fixup(f):  # type: (Text) -> Text
 
     return doc
 
+
 def draft3toDraft4dev1(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     """Public updater for draft-3 to draft-4.dev1."""
     return (_draft3toDraft4dev1(doc, loader, baseuri), "draft-4.dev1")
 
+
 def _draft4Dev1toDev2(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Any
     if isinstance(doc, dict):
@@ -389,6 +398,7 @@ def _draft4Dev1toDev2(doc, loader, baseuri):
 
     return doc
 
+
 def draft4Dev1toDev2(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     """Public updater for draft-4.dev1 to draft-4.dev2."""
@@ -423,11 +433,13 @@ def _draft4Dev2toDev3(doc, loader, baseuri):
 
     return doc
 
+
 def draft4Dev2toDev3(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     """Public updater for draft-4.dev2 to draft-4.dev3."""
     return (_draft4Dev2toDev3(doc, loader, baseuri), "draft-4.dev3")
 
+
 def _draft4Dev3to1_0dev4(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Any
     if isinstance(doc, dict):
@@ -441,16 +453,19 @@ def _draft4Dev3to1_0dev4(doc, loader, baseuri):
             doc[i] = _draft4Dev3to1_0dev4(a, loader, baseuri)
     return doc
 
+
 def draft4Dev3to1_0dev4(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     """Public updater for draft-4.dev3 to v1.0.dev4."""
     return (_draft4Dev3to1_0dev4(doc, loader, baseuri), "v1.0.dev4")
 
+
 def v1_0dev4to1_0(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     """Public updater for v1.0.dev4 to v1.0."""
     return (doc, "v1.0")
 
+
 def v1_0to1_1_0dev1(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Tuple[Any, Text]
     """Public updater for v1.0 to v1.1.0-dev1."""
@@ -482,11 +497,13 @@ def v1_0to1_1_0dev1(doc, loader, baseuri):
 
 LATEST = "v1.0"
 
+
 def identity(doc, loader, baseuri):  # pylint: disable=unused-argument
     # type: (Any, Loader, Text) -> Tuple[Any, Union[Text, Text]]
     """The default, do-nothing, CWL document upgrade function."""
     return (doc, doc["cwlVersion"])
 
+
 def checkversion(doc, metadata, enable_dev):
     # type: (Union[CommentedSeq, CommentedMap], CommentedMap, bool) -> Tuple[Dict[Text, Any], Text]  # pylint: disable=line-too-long
     """Checks the validity of the version of the give CWL document.
@@ -526,6 +543,7 @@ def checkversion(doc, metadata, enable_dev):
 
     return (cdoc, version)
 
+
 def update(doc, loader, baseuri, enable_dev, metadata):
     # type: (Union[CommentedSeq, CommentedMap], Loader, Text, bool, Any) -> dict
 
diff --git a/cwltool/utils.py b/cwltool/utils.py
index 2f1abf31a..8f341c0a9 100644
--- a/cwltool/utils.py
+++ b/cwltool/utils.py
@@ -2,12 +2,14 @@
 
 from typing import Any, Tuple
 
+
 def aslist(l):  # type: (Any) -> List[Any]
     if isinstance(l, list):
         return l
     else:
         return [l]
 
+
 def get_feature(self, feature):  # type: (Any, Any) -> Tuple[Any, bool]
     for t in reversed(self.requirements):
         if t["class"] == feature:
diff --git a/cwltool/workflow.py b/cwltool/workflow.py
index 16912a0e1..0e4f59739 100644
--- a/cwltool/workflow.py
+++ b/cwltool/workflow.py
@@ -1,32 +1,27 @@
 import copy
+import functools
+import json
 import logging
 import random
-import os
-from collections import namedtuple
-import functools
-import urlparse
 import tempfile
-import shutil
-import json
-
-from typing import Any, Callable, cast, Generator, Iterable, List, Text, Union
+from collections import namedtuple
 
 import schema_salad.validate as validate
 from schema_salad.sourceline import SourceLine
+from typing import Any, Callable, cast, Generator, Iterable, List, Text, Union
 
-from . import job
 from . import draft2tool
-from .utils import aslist
-from .process import Process, get_feature, empty_subtree, shortname, uniquename
-from .errors import WorkflowException
 from . import expression
+from .errors import WorkflowException
 from .load_tool import load_tool
-
+from .process import Process, shortname, uniquename
+from .utils import aslist
 
 _logger = logging.getLogger("cwltool")
 
 WorkflowStateItem = namedtuple('WorkflowStateItem', ['parameter', 'value'])
 
+
 def defaultMakeTool(toolpath_object, **kwargs):
     # type: (Dict[Text, Any], **Any) -> Process
     if not isinstance(toolpath_object, dict):
@@ -39,7 +34,10 @@ def defaultMakeTool(toolpath_object, **kwargs):
         elif toolpath_object["class"] == "Workflow":
             return Workflow(toolpath_object, **kwargs)
 
-    raise WorkflowException(u"Missing or invalid 'class' field in %s, expecting one of: CommandLineTool, ExpressionTool, Workflow" % toolpath_object["id"])
+    raise WorkflowException(
+        u"Missing or invalid 'class' field in %s, expecting one of: CommandLineTool, ExpressionTool, Workflow" %
+        toolpath_object["id"])
+
 
 def findfiles(wo, fn=None):  # type: (Any, List) -> List[Dict[Text, Any]]
     if fn is None:
@@ -74,24 +72,25 @@ def match_types(sinktype, src, iid, inputobj, linkMerge, valueFrom):
                 return False
         return True
     elif linkMerge:
-            if iid not in inputobj:
-                inputobj[iid] = []
-            if linkMerge == "merge_nested":
-                inputobj[iid].append(src.value)
-            elif linkMerge == "merge_flattened":
-                if isinstance(src.value, list):
-                    inputobj[iid].extend(src.value)
-                else:
-                    inputobj[iid].append(src.value)
+        if iid not in inputobj:
+            inputobj[iid] = []
+        if linkMerge == "merge_nested":
+            inputobj[iid].append(src.value)
+        elif linkMerge == "merge_flattened":
+            if isinstance(src.value, list):
+                inputobj[iid].extend(src.value)
             else:
-                raise WorkflowException(u"Unrecognized linkMerge enum '%s'" % linkMerge)
-            return True
+                inputobj[iid].append(src.value)
+        else:
+            raise WorkflowException(u"Unrecognized linkMerge enum '%s'" % linkMerge)
+        return True
     elif valueFrom is not None or can_assign_src_to_sink(src.parameter["type"], sinktype) or sinktype == "Any":
         # simply assign the value from state to input
         inputobj[iid] = copy.deepcopy(src.value)
         return True
     return False
 
+
 def can_assign_src_to_sink(src, sink):  # type: (Any, Any) -> bool
     """Check for identical type specifications, ignoring extra keys like inputBinding.
     """
@@ -114,6 +113,7 @@ def can_assign_src_to_sink(src, sink):  # type: (Any, Any) -> bool
         return src == sink
     return False
 
+
 def _compare_records(src, sink):
     # type: (Dict[Text, Any], Dict[Text, Any]) -> bool
     """Compare two records, ensuring they have compatible fields.
@@ -121,6 +121,7 @@ def _compare_records(src, sink):
     This handles normalizing record names, which will be relative to workflow
     step, so that they can be compared.
     """
+
     def _rec_fields(rec):  # type: (Dict[Text, Any]) -> Dict[Text, Any]
         out = {}
         for field in rec["fields"]:
@@ -133,14 +134,15 @@ def _rec_fields(rec):  # type: (Dict[Text, Any]) -> Dict[Text, Any]
     for key in sinkfields.iterkeys():
         if (not can_assign_src_to_sink(
                 srcfields.get(key, "null"), sinkfields.get(key, "null"))
-                and sinkfields.get(key) is not None):
+            and sinkfields.get(key) is not None):
             _logger.info("Record comparison failure for %s and %s\n"
                          "Did not match fields for %s: %s and %s" %
                          (src["name"], sink["name"], key, srcfields.get(key),
-                             sinkfields.get(key)))
+                          sinkfields.get(key)))
             return False
     return True
 
+
 def object_from_state(state, parms, frag_only, supportsMultipleInput, sourceField, incomplete=False):
     # type: (Dict[Text, WorkflowStateItem], List[Dict[Text, Any]], bool, bool, Text, bool) -> Dict[Text, Any]
     inputobj = {}  # type: Dict[Text, Any]
@@ -150,7 +152,7 @@ def object_from_state(state, parms, frag_only, supportsMultipleInput, sourceFiel
             iid = shortname(iid)
         if sourceField in inp:
             if (isinstance(inp[sourceField], list) and not
-                    supportsMultipleInput):
+            supportsMultipleInput):
                 raise WorkflowException(
                     "Workflow contains multiple inbound links to a single "
                     "parameter but MultipleInputFeatureRequirement is not "
@@ -161,13 +163,13 @@ def object_from_state(state, parms, frag_only, supportsMultipleInput, sourceFiel
                     if not match_types(
                             inp["type"], state[src], iid, inputobj,
                             inp.get("linkMerge", ("merge_nested"
-                                if len(connections) > 1 else None)),
+                                                  if len(connections) > 1 else None)),
                             valueFrom=inp.get("valueFrom")):
                         raise WorkflowException(
                             u"Type mismatch between source '%s' (%s) and "
                             "sink '%s' (%s)" % (src,
-                                state[src].parameter["type"], inp["id"],
-                                inp["type"]))
+                                                state[src].parameter["type"], inp["id"],
+                                                inp["type"]))
                 elif src not in state:
                     raise WorkflowException(
                         u"Connect source '%s' on parameter '%s' does not "
@@ -184,7 +186,6 @@ def object_from_state(state, parms, frag_only, supportsMultipleInput, sourceFiel
 
 
 class WorkflowJobStep(object):
-
     def __init__(self, step):  # type: (Any) -> None
         self.step = step
         self.tool = step.tool
@@ -203,7 +204,6 @@ def job(self, joborder, output_callback, **kwargs):
 
 
 class WorkflowJob(object):
-
     def __init__(self, workflow, **kwargs):
         # type: (Workflow, **Any) -> None
         self.workflow = workflow
@@ -221,7 +221,8 @@ def __init__(self, workflow, **kwargs):
 
         self.name = uniquename(u"workflow %s" % kwargs.get("name", shortname(self.workflow.tool.get("id", "embedded"))))
 
-        _logger.debug(u"[%s] initialized from %s", self.name, self.tool.get("id", "workflow embedded in %s" % kwargs.get("part_of")))
+        _logger.debug(u"[%s] initialized from %s", self.name,
+                      self.tool.get("id", "workflow embedded in %s" % kwargs.get("part_of")))
 
     def receive_output(self, step, outputparms, jobout, processStatus):
         # type: (WorkflowJobStep, List[Dict[Text,Text]], Dict[Text,Text], Text) -> None
@@ -275,13 +276,14 @@ def try_make_job(self, step, **kwargs):
                 if "valueFrom" in i}
 
             if len(valueFrom) > 0 and not bool(self.workflow.get_requirement("StepInputExpressionRequirement")[0]):
-                raise WorkflowException("Workflow step contains valueFrom but StepInputExpressionRequirement not in requirements")
+                raise WorkflowException(
+                    "Workflow step contains valueFrom but StepInputExpressionRequirement not in requirements")
 
-            vfinputs = {shortname(k): v for k,v in inputobj.iteritems()}
+            vfinputs = {shortname(k): v for k, v in inputobj.iteritems()}
 
             def postScatterEval(io):
                 # type: (Dict[Text, Any]) -> Dict[Text, Any]
-                shortio = {shortname(k): v for k,v in io.iteritems()}
+                shortio = {shortname(k): v for k, v in io.iteritems()}
 
                 def valueFromFunc(k, v):  # type: (Any, Any) -> Any
                     if k in valueFrom:
@@ -290,7 +292,8 @@ def valueFromFunc(k, v):  # type: (Any, Any) -> Any
                             None, None, {}, context=v)
                     else:
                         return v
-                return {k: valueFromFunc(k, v) for k,v in io.items()}
+
+                return {k: valueFromFunc(k, v) for k, v in io.items()}
 
             if "scatter" in step.tool:
                 scatter = aslist(step.tool["scatter"])
@@ -303,20 +306,20 @@ def valueFromFunc(k, v):  # type: (Any, Any) -> Any
                     jobs = dotproduct_scatter(step, inputobj, scatter,
                                               cast(  # known bug with mypy
                                                   # https://github.com/python/mypy/issues/797
-                                                  Callable[[Any], Any],callback), **kwargs)
+                                                  Callable[[Any], Any], callback), **kwargs)
                 elif method == "nested_crossproduct":
                     jobs = nested_crossproduct_scatter(step, inputobj,
-                        scatter, cast(Callable[[Any], Any], callback),
-                        # known bug in mypy
-                        # https://github.com/python/mypy/issues/797
-                        **kwargs)
+                                                       scatter, cast(Callable[[Any], Any], callback),
+                                                       # known bug in mypy
+                                                       # https://github.com/python/mypy/issues/797
+                                                       **kwargs)
                 elif method == "flat_crossproduct":
                     jobs = cast(Generator,
                                 flat_crossproduct_scatter(step, inputobj,
                                                           scatter,
                                                           cast(Callable[[Any], Any],
-                                                         # known bug in mypy
-                                                         # https://github.com/python/mypy/issues/797
+                                                               # known bug in mypy
+                                                               # https://github.com/python/mypy/issues/797
                                                                callback), 0, **kwargs))
             else:
                 if _logger.isEnabledFor(logging.DEBUG):
@@ -358,7 +361,8 @@ def job(self, joborder, output_callback, **kwargs):
                 elif "default" in i:
                     self.state[i["id"]] = WorkflowStateItem(i, copy.deepcopy(i["default"]))
                 else:
-                    raise WorkflowException(u"Input '%s' not in input object and does not have a default value." % (i["id"]))
+                    raise WorkflowException(
+                        u"Input '%s' not in input object and does not have a default value." % (i["id"]))
 
         for s in self.steps:
             for out in s.tool["outputs"]:
@@ -406,7 +410,8 @@ def job(self, joborder, output_callback, **kwargs):
         supportsMultipleInput = bool(self.workflow.get_requirement("MultipleInputFeatureRequirement")[0])
 
         try:
-            wo = object_from_state(self.state, self.tool["outputs"], True, supportsMultipleInput, "outputSource", incomplete=True)
+            wo = object_from_state(self.state, self.tool["outputs"], True, supportsMultipleInput, "outputSource",
+                                   incomplete=True)
         except WorkflowException as e:
             _logger.error(u"[%s] Cannot collect workflow output: %s", self.name, e)
             wo = {}
@@ -426,7 +431,7 @@ def __init__(self, toolpath_object, **kwargs):
         kwargs["hints"] = self.hints
 
         makeTool = kwargs.get("makeTool")
-        self.steps = [WorkflowStep(step, n, **kwargs) for n,step in enumerate(self.tool.get("steps", []))]
+        self.steps = [WorkflowStep(step, n, **kwargs) for n, step in enumerate(self.tool.get("steps", []))]
         random.shuffle(self.steps)
 
         # TODO: statically validate data links instead of doing it at runtime.
@@ -449,7 +454,6 @@ def visit(self, op):
 
 
 class WorkflowStep(Process):
-
     def __init__(self, toolpath_object, pos, **kwargs):
         # type: (Dict[Text, Any], int, **Any) -> None
         if "id" in toolpath_object:
@@ -497,8 +501,11 @@ def __init__(self, toolpath_object, pos, **kwargs):
                     if stepfield == "in":
                         param["type"] = "Any"
                     else:
-                        raise WorkflowException("[%s] Workflow step output '%s' not found in the outputs of the tool (expected one of '%s')" % (
-                            self.id, shortname(step_entry), "', '".join([shortname(tool_entry["id"]) for tool_entry in self.embedded_tool.tool[toolfield]])))
+                        raise WorkflowException(
+                            "[%s] Workflow step output '%s' not found in the outputs of the tool (expected one of '%s')" % (
+                                self.id, shortname(step_entry), "', '".join(
+                                    [shortname(tool_entry["id"]) for tool_entry in
+                                     self.embedded_tool.tool[toolfield]])))
                 param["id"] = inputid
                 toolpath_object[toolfield].append(param)
 
@@ -507,7 +514,8 @@ def __init__(self, toolpath_object, pos, **kwargs):
         if self.embedded_tool.tool["class"] == "Workflow":
             (feature, _) = self.get_requirement("SubworkflowFeatureRequirement")
             if not feature:
-                raise WorkflowException("Workflow contains embedded workflow but SubworkflowFeatureRequirement not in requirements")
+                raise WorkflowException(
+                    "Workflow contains embedded workflow but SubworkflowFeatureRequirement not in requirements")
 
         if "scatter" in self.tool:
             (feature, _) = self.get_requirement("ScatterFeatureRequirement")
@@ -525,7 +533,8 @@ def __init__(self, toolpath_object, pos, **kwargs):
             inp_map = {i["id"]: i for i in inputparms}
             for s in scatter:
                 if s not in inp_map:
-                    raise WorkflowException(u"Scatter parameter '%s' does not correspond to an input parameter of this step, inputs are %s" % (s, inp_map.keys()))
+                    raise WorkflowException(u"Scatter parameter '%s' does not correspond to an input parameter of this "
+                                            u"step, inputs are %s" % (s, inp_map.keys()))
 
                 inp_map[s]["type"] = {"type": "array", "items": inp_map[s]["type"]}
 
@@ -542,7 +551,7 @@ def __init__(self, toolpath_object, pos, **kwargs):
 
     def receive_output(self, output_callback, jobout, processStatus):
         # type: (Callable[...,Any], Dict[Text, Text], Text) -> None
-        #_logger.debug("WorkflowStep output from run is %s", jobout)
+        # _logger.debug("WorkflowStep output from run is %s", jobout)
         output = {}
         for i in self.tool["outputs"]:
             field = shortname(i["id"])
@@ -577,7 +586,6 @@ def visit(self, op):
 
 
 class ReceiveScatterOutput(object):
-
     def __init__(self, output_callback, dest):
         # type: (Callable[..., Any], Dict[Text,List[Text]]) -> None
         self.dest = dest
@@ -588,7 +596,7 @@ def __init__(self, output_callback, dest):
 
     def receive_scatter_output(self, index, jobout, processStatus):
         # type: (int, Dict[Text, Text], Text) -> None
-        for k,v in jobout.items():
+        for k, v in jobout.items():
             self.dest[k][index] = v
 
         if processStatus != "success":
@@ -605,6 +613,7 @@ def setTotal(self, total):  # type: (int) -> None
         if self.completed == self.total:
             self.output_callback(self.dest, self.processStatus)
 
+
 def parallel_steps(steps, rc, kwargs):  # type: (List[Generator], ReceiveScatterOutput, Dict[str, Any]) -> Generator
     while rc.completed < rc.total:
         made_progress = False
@@ -628,6 +637,7 @@ def parallel_steps(steps, rc, kwargs):  # type: (List[Generator], ReceiveScatter
         if not made_progress and rc.completed < rc.total:
             yield None
 
+
 def dotproduct_scatter(process, joborder, scatter_keys, output_callback, **kwargs):
     # type: (WorkflowJobStep, Dict[Text, Any], List[Text], Callable[..., Any], **Any) -> Generator
     l = None
@@ -677,16 +687,17 @@ def nested_crossproduct_scatter(process, joborder, scatter_keys, output_callback
             jo = kwargs["postScatterEval"](jo)
             steps.append(process.job(jo, functools.partial(rc.receive_scatter_output, n), **kwargs))
         else:
+            # known bug with mypy, https://github.com/python/mypy/issues/797
+            casted = cast(Callable[[Any], Any], functools.partial(rc.receive_scatter_output, n))
             steps.append(nested_crossproduct_scatter(process, jo,
-                    scatter_keys[1:], cast(  # known bug with mypy
-                        # https://github.com/python/mypy/issues/797g
-                        Callable[[Any], Any],
-                        functools.partial(rc.receive_scatter_output, n)), **kwargs))
+                                                     scatter_keys[1:],
+                                                     casted, **kwargs))
 
     rc.setTotal(l)
 
     return parallel_steps(steps, rc, kwargs)
 
+
 def crossproduct_size(joborder, scatter_keys):
     # type: (Dict[Text, Any], List[Text]) -> int
     scatter_key = scatter_keys[0]
@@ -700,6 +711,7 @@ def crossproduct_size(joborder, scatter_keys):
             sum += crossproduct_size(joborder, scatter_keys[1:])
     return sum
 
+
 def flat_crossproduct_scatter(process, joborder, scatter_keys, output_callback, startindex, **kwargs):
     # type: (WorkflowJobStep, Dict[Text, Any], List[Text], Union[ReceiveScatterOutput,Callable[..., Any]], int, **Any) -> Union[List[Generator], Generator]
     scatter_key = scatter_keys[0]
diff --git a/ez_setup.py b/ez_setup.py
index 50e0dfc69..e4e7b6ee9 100755
--- a/ez_setup.py
+++ b/ez_setup.py
@@ -6,18 +6,16 @@
 Run this script to install or upgrade setuptools.
 """
 
+import contextlib
+import optparse
 import os
+import platform
 import shutil
+import subprocess
 import sys
 import tempfile
-import zipfile
-import optparse
-import subprocess
-import platform
 import textwrap
-import contextlib
-import warnings
-
+import zipfile
 from distutils import log
 
 try:
@@ -70,7 +68,6 @@ def _build_egg(egg, archive_filename, to_dir):
 
 
 class ContextualZipFile(zipfile.ZipFile):
-
     """Supplement ZipFile class to support context manager for Python 2.6."""
 
     def __enter__(self):
@@ -176,13 +173,13 @@ def _conflict_bail(VC_err, version):
     unsafe to unload it. Bail out.
     """
     conflict_tmpl = textwrap.dedent("""
-        The required version of setuptools (>={version}) is not available,
-        and can't be installed while this script is running. Please
-        install a more recent version first, using
-        'easy_install -U setuptools'.
+		The required version of setuptools (>={version}) is not available,
+		and can't be installed while this script is running. Please
+		install a more recent version first, using
+		'easy_install -U setuptools'.
 
-        (Currently using {VC_err.args[0]!r})
-        """)
+		(Currently using {VC_err.args[0]!r})
+		""")
     msg = conflict_tmpl.format(**locals())
     sys.stderr.write(msg)
     sys.exit(2)
@@ -192,7 +189,7 @@ def _unload_pkg_resources():
     del_modules = [
         name for name in sys.modules
         if name.startswith('pkg_resources')
-    ]
+        ]
     for mod_name in del_modules:
         del sys.modules[mod_name]
 
@@ -244,6 +241,8 @@ def has_powershell():
         except Exception:
             return False
     return True
+
+
 download_file_powershell.viable = has_powershell
 
 
@@ -260,6 +259,8 @@ def has_curl():
         except Exception:
             return False
     return True
+
+
 download_file_curl.viable = has_curl
 
 
@@ -276,6 +277,8 @@ def has_wget():
         except Exception:
             return False
     return True
+
+
 download_file_wget.viable = has_wget
 
 
@@ -291,6 +294,8 @@ def download_file_insecure(url, target):
     # Write all the data in one block to avoid creating a partial file.
     with open(target, "wb") as dst:
         dst.write(data)
+
+
 download_file_insecure.viable = lambda: True
 
 
@@ -362,9 +367,9 @@ def _parse_args():
         default=DEFAULT_VERSION,
     )
     parser.add_option(
-    	'--to-dir',
-    	help="Directory to save (and re-use) package",
-    	default=DEFAULT_SAVE_DIR,
+        '--to-dir',
+        help="Directory to save (and re-use) package",
+        default=DEFAULT_SAVE_DIR,
     )
     options, args = parser.parse_args()
     # positional arguments are ignored
@@ -372,13 +377,13 @@ def _parse_args():
 
 
 def _download_args(options):
-	"""Return args for download_setuptools function from cmdline args."""
-	return dict(
-		version=options.version,
-		download_base=options.download_base,
-		downloader_factory=options.downloader_factory,
-		to_dir=options.to_dir,
-	)
+    """Return args for download_setuptools function from cmdline args."""
+    return dict(
+        version=options.version,
+        download_base=options.download_base,
+        downloader_factory=options.downloader_factory,
+        to_dir=options.to_dir,
+    )
 
 
 def main():
@@ -387,5 +392,6 @@ def main():
     archive = download_setuptools(**_download_args(options))
     return _install(archive, _build_install_args(options))
 
+
 if __name__ == '__main__':
     sys.exit(main())
diff --git a/gittaggers.py b/gittaggers.py
index 53dda8fd8..d15f6886f 100644
--- a/gittaggers.py
+++ b/gittaggers.py
@@ -1,10 +1,10 @@
-from setuptools.command.egg_info import egg_info
 import subprocess
 import time
 
+from setuptools.command.egg_info import egg_info
+
 
 class EggInfoFromGit(egg_info):
-
     """Tag the build with git commit timestamp.
 
     If a build tag has already been set (e.g., "egg_info -b", building
diff --git a/setup.py b/setup.py
index a3d610648..72c57d387 100755
--- a/setup.py
+++ b/setup.py
@@ -1,18 +1,18 @@
 #!/usr/bin/env python
 import ez_setup
+
 ez_setup.use_setuptools()
 import os
-import sys
-import shutil
 
 import setuptools.command.egg_info as egg_info_cmd
-from setuptools import setup, find_packages
+from setuptools import setup
 
 SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, 'README.rst')
 
 try:
     import gittaggers
+
     tagger = gittaggers.EggInfoFromGit
 except ImportError:
     tagger = egg_info_cmd.egg_info
@@ -53,8 +53,8 @@
       test_suite='tests',
       tests_require=[],
       entry_points={
-          'console_scripts': [ "cwltool=cwltool.main:main" ]
+          'console_scripts': ["cwltool=cwltool.main:main"]
       },
       zip_safe=True,
       cmdclass={'egg_info': tagger},
-)
+      )
diff --git a/tests/test_examples.py b/tests/test_examples.py
index a133c7b0f..794a11b30 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -1,14 +1,13 @@
 import unittest
-import json
-import cwltool.draft2tool as tool
+
 import cwltool.expression as expr
 import cwltool.factory
-import cwltool.process
 import cwltool.pathmapper
+import cwltool.process
 import cwltool.workflow
 
-class TestParamMatching(unittest.TestCase):
 
+class TestParamMatching(unittest.TestCase):
     def test_params(self):
         self.assertTrue(expr.param_re.match("(foo)"))
         self.assertTrue(expr.param_re.match("(foo.bar)"))
@@ -52,19 +51,19 @@ def test_params(self):
                 }
             },
             "lst": ["A", "B"]
-         }
+        }
 
         self.assertEqual(expr.interpolate("$(foo)", inputs), inputs["foo"])
 
         for pattern in ("$(foo.bar)",
-                         "$(foo['bar'])",
-                         "$(foo[\"bar\"])"):
+                        "$(foo['bar'])",
+                        "$(foo[\"bar\"])"):
             self.assertEqual(expr.interpolate(pattern, inputs), inputs["foo"]["bar"])
 
         for pattern in ("$(foo.bar.baz)",
-                         "$(foo['bar'].baz)",
-                         "$(foo['bar'][\"baz\"])",
-                         "$(foo.bar['baz'])"):
+                        "$(foo['bar'].baz)",
+                        "$(foo['bar'][\"baz\"])",
+                        "$(foo.bar['baz'])"):
             self.assertEqual(expr.interpolate(pattern, inputs), "zab1")
 
         self.assertEqual(expr.interpolate("$(foo['b ar'].baz)", inputs), 2)
@@ -78,14 +77,14 @@ def test_params(self):
         self.assertEqual(expr.interpolate("$(lst['length'])", inputs), 2)
 
         for pattern in ("-$(foo.bar)",
-                         "-$(foo['bar'])",
-                         "-$(foo[\"bar\"])"):
+                        "-$(foo['bar'])",
+                        "-$(foo[\"bar\"])"):
             self.assertEqual(expr.interpolate(pattern, inputs), """-{"baz": "zab1"}""")
 
         for pattern in ("-$(foo.bar.baz)",
-                         "-$(foo['bar'].baz)",
-                         "-$(foo['bar'][\"baz\"])",
-                         "-$(foo.bar['baz'])"):
+                        "-$(foo['bar'].baz)",
+                        "-$(foo['bar'][\"baz\"])",
+                        "-$(foo.bar['baz'])"):
             self.assertEqual(expr.interpolate(pattern, inputs), "-zab1")
 
         self.assertEqual(expr.interpolate("-$(foo['b ar'].baz)", inputs), "-2")
@@ -93,16 +92,15 @@ def test_params(self):
         self.assertEqual(expr.interpolate("-$(foo[\"b\\'ar\"].baz)", inputs), "-true")
         self.assertEqual(expr.interpolate("-$(foo['b\\\"ar'].baz)", inputs), "-null")
 
-
         for pattern in ("$(foo.bar) $(foo.bar)",
-                         "$(foo['bar']) $(foo['bar'])",
-                         "$(foo[\"bar\"]) $(foo[\"bar\"])"):
+                        "$(foo['bar']) $(foo['bar'])",
+                        "$(foo[\"bar\"]) $(foo[\"bar\"])"):
             self.assertEqual(expr.interpolate(pattern, inputs), """{"baz": "zab1"} {"baz": "zab1"}""")
 
         for pattern in ("$(foo.bar.baz) $(foo.bar.baz)",
-                         "$(foo['bar'].baz) $(foo['bar'].baz)",
-                         "$(foo['bar'][\"baz\"]) $(foo['bar'][\"baz\"])",
-                         "$(foo.bar['baz']) $(foo.bar['baz'])"):
+                        "$(foo['bar'].baz) $(foo['bar'].baz)",
+                        "$(foo['bar'][\"baz\"]) $(foo['bar'][\"baz\"])",
+                        "$(foo.bar['baz']) $(foo.bar['baz'])"):
             self.assertEqual(expr.interpolate(pattern, inputs), "zab1 zab1")
 
         self.assertEqual(expr.interpolate("$(foo['b ar'].baz) $(foo['b ar'].baz)", inputs), "2 2")
@@ -110,8 +108,8 @@ def test_params(self):
         self.assertEqual(expr.interpolate("$(foo[\"b\\'ar\"].baz) $(foo[\"b\\'ar\"].baz)", inputs), "true true")
         self.assertEqual(expr.interpolate("$(foo['b\\\"ar'].baz) $(foo['b\\\"ar'].baz)", inputs), "null null")
 
-class TestFactory(unittest.TestCase):
 
+class TestFactory(unittest.TestCase):
     def test_factory(self):
         f = cwltool.factory.Factory()
         echo = f.make("tests/echo.cwl")
@@ -140,6 +138,7 @@ def test_partial_output(self):
         else:
             self.fail("Should have raised WorkflowStatus")
 
+
 class TestScanDeps(unittest.TestCase):
     def test_scandeps(self):
         obj = {
@@ -198,9 +197,9 @@ def loadref(base, p):
                 raise Exception("test case can't load things")
 
         sc = cwltool.process.scandeps(obj["id"], obj,
-                                       set(("$import", "run")),
-                                       set(("$include", "$schemas", "location")),
-                                                  loadref)
+                                      {"$import", "run"},
+                                      {"$include", "$schemas", "location"},
+                                      loadref)
 
         sc.sort(key=lambda k: k["basename"])
 
@@ -209,34 +208,34 @@ def loadref(base, p):
             "class": "File",
             "location": "file:///example/bar.cwl"
         },
-        {
-            "basename": "data.txt",
-            "class": "File",
-            "location": "file:///example/data.txt"
-        },
-        {
-            "basename": "data2",
-            "class": "Directory",
-            "location": "file:///example/data2",
-            "listing": [{
-                "basename": "data3.txt",
+            {
+                "basename": "data.txt",
                 "class": "File",
-                "location": "file:///example/data3.txt",
-                "secondaryFiles": [{
+                "location": "file:///example/data.txt"
+            },
+            {
+                "basename": "data2",
+                "class": "Directory",
+                "location": "file:///example/data2",
+                "listing": [{
+                    "basename": "data3.txt",
                     "class": "File",
-                    "basename": "data5.txt",
-                    "location": "file:///example/data5.txt"
+                    "location": "file:///example/data3.txt",
+                    "secondaryFiles": [{
+                        "class": "File",
+                        "basename": "data5.txt",
+                        "location": "file:///example/data5.txt"
+                    }]
                 }]
-            }]
-        }, {
+            }, {
                 "basename": "data4.txt",
                 "class": "File",
                 "location": "file:///example/data4.txt"
-        }], sc)
+            }], sc)
 
         sc = cwltool.process.scandeps(obj["id"], obj,
-                                       set(("run"),),
-                                       set(), loadref)
+                                      set(("run"), ),
+                                      set(), loadref)
 
         sc.sort(key=lambda k: k["basename"])
 
@@ -246,41 +245,42 @@ def loadref(base, p):
             "location": "file:///example/bar.cwl"
         }], sc)
 
+
 class TestDedup(unittest.TestCase):
     def test_dedup(self):
         ex = [{
             "class": "File",
             "location": "file:///example/a"
         },
-        {
-            "class": "File",
-            "location": "file:///example/a"
-        },
-        {
-            "class": "File",
-            "location": "file:///example/d"
-        },
-        {
-            "class": "Directory",
-            "location": "file:///example/c",
-            "listing": [{
+            {
+                "class": "File",
+                "location": "file:///example/a"
+            },
+            {
                 "class": "File",
                 "location": "file:///example/d"
+            },
+            {
+                "class": "Directory",
+                "location": "file:///example/c",
+                "listing": [{
+                    "class": "File",
+                    "location": "file:///example/d"
+                }]
             }]
-        }]
 
         self.assertEquals([{
             "class": "File",
             "location": "file:///example/a"
         },
-        {
-            "class": "Directory",
-            "location": "file:///example/c",
-            "listing": [{
-                "class": "File",
-                "location": "file:///example/d"
-            }]
-        }], cwltool.pathmapper.dedup(ex))
+            {
+                "class": "Directory",
+                "location": "file:///example/c",
+                "listing": [{
+                    "class": "File",
+                    "location": "file:///example/d"
+                }]
+            }], cwltool.pathmapper.dedup(ex))
 
 
 class TestTypeCompare(unittest.TestCase):
@@ -304,31 +304,30 @@ def test_typecompare(self):
     def test_recordcompare(self):
         src = {
             'fields': [{
-                'type': { 'items': 'string', 'type': 'array' },
+                'type': {'items': 'string', 'type': 'array'},
                 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/description'
             },
-            {
-                'type': { 'items': 'File', 'type': 'array' },
-                'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/vrn_file'
-            }],
-               'type': 'record',
-               'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec'
+                {
+                    'type': {'items': 'File', 'type': 'array'},
+                    'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/vrn_file'
+                }],
+            'type': 'record',
+            'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec'
         }
         sink = {
             'fields': [{
                 'type': {'items': 'string', 'type': 'array'},
                 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/description'
             },
-            {
-                'type': {'items': 'File', 'type': 'array'},
-                'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/vrn_file'
-            }],
+                {
+                    'type': {'items': 'File', 'type': 'array'},
+                    'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/vrn_file'
+                }],
             'type': 'record',
             'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec'}
 
         self.assertTrue(cwltool.workflow.can_assign_src_to_sink(src, sink))
 
-
     def test_lifting(self):
         # check that lifting the types of the process outputs to the workflow step
         # fails if the step 'out' doesn't match.
diff --git a/tests/test_fetch.py b/tests/test_fetch.py
index 2a0f06870..7845fb9b6 100644
--- a/tests/test_fetch.py
+++ b/tests/test_fetch.py
@@ -1,17 +1,13 @@
 import unittest
-import schema_salad.ref_resolver
+
 import schema_salad.main
+import schema_salad.ref_resolver
 import schema_salad.schema
-from schema_salad.jsonld_context import makerdf
-from pkg_resources import Requirement, resource_filename, ResolutionError  # type: ignore
-import rdflib
-import ruamel.yaml as yaml
-import json
-import os
 
+from cwltool.load_tool import load_tool
 from cwltool.main import main
 from cwltool.workflow import defaultMakeTool
-from cwltool.load_tool import load_tool
+
 
 class FetcherTest(unittest.TestCase):
     def test_fetcher(self):
@@ -19,7 +15,7 @@ class TestFetcher(schema_salad.ref_resolver.Fetcher):
             def __init__(self, a, b):
                 pass
 
-            def fetch_text(self, url):    # type: (unicode) -> unicode
+            def fetch_text(self, url):  # type: (unicode) -> unicode
                 if url == "baz:bar/foo.cwl":
                     return """
 cwlVersion: v1.0
@@ -42,4 +38,5 @@ def test_resolver(d, a):
 
         load_tool("foo.cwl", defaultMakeTool, resolver=test_resolver, fetcher_constructor=TestFetcher)
 
-        self.assertEquals(0, main(["--print-pre", "--debug", "foo.cwl"], resolver=test_resolver, fetcher_constructor=TestFetcher))
+        self.assertEquals(0, main(["--print-pre", "--debug", "foo.cwl"], resolver=test_resolver,
+                                  fetcher_constructor=TestFetcher))
diff --git a/tests/test_pack.py b/tests/test_pack.py
index dd4fad476..7193cd054 100644
--- a/tests/test_pack.py
+++ b/tests/test_pack.py
@@ -1,11 +1,11 @@
-import unittest
 import json
 import os
+import unittest
 from functools import partial
 
-from cwltool.load_tool import fetch_document, validate_document
 import cwltool.pack
 import cwltool.workflow
+from cwltool.load_tool import fetch_document, validate_document
 from cwltool.main import makeRelative
 from cwltool.process import adjustFileObjs, adjustDirObjs
 
diff --git a/tests/test_pathmapper.py b/tests/test_pathmapper.py
index b54c89a3f..a5302140a 100644
--- a/tests/test_pathmapper.py
+++ b/tests/test_pathmapper.py
@@ -1,17 +1,11 @@
 import unittest
-import json
-import cwltool.draft2tool as tool
-import cwltool.expression as expr
-import cwltool.factory
+
 from cwltool.pathmapper import PathMapper
 
 
 class TestPathMapper(unittest.TestCase):
-
     def test_subclass(self):
-
         class SubPathMapper(PathMapper):
-
             def __init__(self, referenced_files, basedir, stagedir, new):
                 super(SubPathMapper, self).__init__(referenced_files, basedir, stagedir)
                 self.new = new
diff --git a/tests/test_relax_path_checks.py b/tests/test_relax_path_checks.py
index 403d8e97e..4012d0a1e 100644
--- a/tests/test_relax_path_checks.py
+++ b/tests/test_relax_path_checks.py
@@ -1,12 +1,11 @@
 import unittest
 from tempfile import NamedTemporaryFile
+
 from cwltool.main import main
 
 
 class ToolArgparse(unittest.TestCase):
-
-
-    script='''
+    script = '''
 #!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
@@ -33,7 +32,8 @@ def test_spaces_in_input_files(self):
                     main(["--debug", f.name, '--input', spaces.name]), 1)
                 self.assertEquals(
                     main(["--debug", "--relax-path-checks", f.name, '--input',
-                        spaces.name]), 0)
+                          spaces.name]), 0)
+
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/tests/test_toolargparse.py b/tests/test_toolargparse.py
index 40983088a..959b630a4 100644
--- a/tests/test_toolargparse.py
+++ b/tests/test_toolargparse.py
@@ -1,12 +1,11 @@
 import unittest
 from tempfile import NamedTemporaryFile
+
 from cwltool.main import main
 
 
 class ToolArgparse(unittest.TestCase):
-
-
-    script='''
+    script = '''
 #!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
@@ -26,7 +25,7 @@ class ToolArgparse(unittest.TestCase):
 baseCommand: [cat]
 '''
 
-    script2='''
+    script2 = '''
 #!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
@@ -44,7 +43,7 @@ class ToolArgparse(unittest.TestCase):
 stdout: foo
 '''
 
-    script3='''
+    script3 = '''
 #!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
@@ -94,11 +93,10 @@ def test_record(self):
             f.flush()
             try:
                 self.assertEquals(main([f.name, '--foo.one', 'README.rst',
-                '--foo.two', 'test']), 0)
+                                        '--foo.two', 'test']), 0)
             except SystemExit as e:
                 self.assertEquals(e.code, 0)
 
 
-
 if __name__ == '__main__':
     unittest.main()