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Patch fix triage #1 #919

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Merged
ewels merged 3 commits into from
Mar 19, 2021
Merged

Patch fix triage #1 #919

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e71d85b
added check for missing emit statement
KevinMenden Mar 19, 2021
95ea08b
fixed conda version warning
KevinMenden Mar 19, 2021
1d3f716
remove extra space
KevinMenden Mar 19, 2021
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8 changes: 4 additions & 4 deletions nf_core/modules/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -261,7 +261,6 @@ def _print_results(self, show_passed=False):

log.debug("Printing final results")
console = Console(force_terminal=rich_force_colors())

# Find maximum module name length
max_mod_name_len = 40
for idx, tests in enumerate([self.passed, self.warned, self.failed]):
Expand Down Expand Up @@ -722,9 +721,9 @@ def check_process_section(self, lines):
# response = _bioconda_package(bp)
response = nf_core.utils.anaconda_package(bp)
except LookupError as e:
self.warned.append(e)
self.warned.append(("bioconda_version", "Conda version not specified correctly", self.main_nf))
except ValueError as e:
self.failed.append(e)
self.failed.append(("bioconda_version", "Conda version not specified correctly", self.main_nf))
else:
# Check that required version is available at all
if bioconda_version not in response.get("versions"):
Expand Down Expand Up @@ -794,7 +793,8 @@ def _parse_output(self, line):
output = []
if "meta" in line:
output.append("meta")
# TODO: should we ignore outputs without emit statement?
if not "emit" in line:
self.failed.append(("missing_emit", f"Missing emit statement: {line.strip()}", self.main_nf))
if "emit" in line:
output.append(line.split("emit:")[1].strip())

Expand Down