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Updated URL for pipeline lint test docs #1451

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merged 2 commits into from
Mar 15, 2022
Merged

Updated URL for pipeline lint test docs #1451

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0e3edff
Updated URL for pipeline lint test docs
ewels Mar 15, 2022
22c5622
Merge branch 'dev' into update-tools-docs-url
ewels Mar 15, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
* Prevent module linting KeyError edge case ([#1321](https://github.com/nf-core/tools/issues/1321))
* Bump-versions: Don't trim the trailing newline on files, causes editorconfig linting to fail ([#1265](https://github.com/nf-core/tools/issues/1265))
* Handle exception in `nf-core list` when a broken git repo is found ([#1273](https://github.com/nf-core/tools/issues/1273))
* Updated URL for pipeline lint test docs ([#1348](https://github.com/nf-core/tools/issues/1348))
* Updated `nf-core create` to tolerate failures and retry when fetching pipeline logos from the website ([#1369](https://github.com/nf-core/tools/issues/1369))

### Modules
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12 changes: 9 additions & 3 deletions nf_core/lint/__init__.py
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Expand Up @@ -12,15 +12,14 @@
import git
import json
import logging
import os
import re
import rich
import rich.progress
import yaml

import nf_core.utils
import nf_core.lint_utils
import nf_core.modules.lint
from nf_core import __version__
from nf_core.lint_utils import console

log = logging.getLogger(__name__)
Expand Down Expand Up @@ -331,7 +330,14 @@ def format_result(test_results, table):
string for the terminal with appropriate ASCII colours.
"""
for eid, msg in test_results:
table.add_row(Markdown("[{0}](https://nf-co.re/tools-docs/lint_tests/{0}.html): {1}".format(eid, msg)))
tools_version = __version__
if "dev" in __version__:
tools_version = "latest"
table.add_row(
Markdown(
f"[{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html): {msg}"
)
)
return table

def _s(some_list):
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