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A few bugfixes #19

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merged 3 commits into from Mar 19, 2018
Merged

A few bugfixes #19

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f0d1f96
A few bugfixes
remiolsen Mar 16, 2018
71949cc
byte literal needs a decode()
remiolsen Mar 16, 2018
589ca66
implemented suggestions by @sven1103
remiolsen Mar 19, 2018
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8 changes: 4 additions & 4 deletions nf_core/lint.py
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Expand Up @@ -104,7 +104,7 @@ def pf(file_path):
files = [files]
if any([os.path.isfile(pf(f)) for f in files]):
self.passed.append((1, "File found: {}".format(files)))
self.files.append(f)
self.files.append(files)
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I think it should be extend(files), as files will be a list.

else:
self.failed.append((1, "File not found: {}".format(files)))

Expand All @@ -114,7 +114,7 @@ def pf(file_path):
files = [files]
if any([os.path.isfile(pf(f)) for f in files]):
self.passed.append((1, "File found: {}".format(files)))
self.files.append(f)
self.files.append(files)
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same here

else:
self.warned.append((1, "File not found: {}".format(files)))

Expand Down Expand Up @@ -210,7 +210,7 @@ def check_config_vars(self):
raise AssertionError("`nextflow config` returned non-zero error code: %s,\n %s", e.returncode, e.output)
else:
for l in nfconfig_raw.splitlines():
k, v = l.split(' = ', 1)
k, v = str(l).split(' = ', 1)
self.config[k] = v
for cf in config_fail:
if cf in self.config.keys():
Expand Down Expand Up @@ -269,7 +269,7 @@ def check_readme(self):
nf_config_version = self.config.get('params.nf_required_version').strip('\'"')
try:
assert nf_badge_version == nf_config_version
except AssertionError, KeyError:
except (AssertionError, KeyError) as e:
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not necessary imo, cause the exception object is not accessed anywhere

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You're right. I guess writing as e is more of a reflex for me 😄

self.failed.append((6, "README Nextflow minimum version badge does not match config. Badge: '{}', Config: '{}'".format(nf_badge_version, nf_config_version)))
else:
self.passed.append((6, "README Nextflow minimum version badge matched config. Badge: '{}', Config: '{}'".format(nf_badge_version, nf_config_version)))
Expand Down