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Fix multiqc_config.yml links #2372

Merged
merged 9 commits into from
Jul 18, 2023
Merged

Fix multiqc_config.yml links #2372

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c50abf4
fix multiqc_config.yml links
mirpedrol Jul 13, 2023
71191da
remove version from multiqc_config.yml and adapt linting accordingly
mirpedrol Jul 13, 2023
02455fc
update changelog
mirpedrol Jul 13, 2023
c62367b
add the version back
mirpedrol Jul 13, 2023
ed4babf
update changelog
mirpedrol Jul 13, 2023
0a35406
Merge branch 'dev' into multiqc-cofig-links
mirpedrol Jul 18, 2023
b670f3a
version in multipqc_config.yml is dev if the version is x.x.xdev
mirpedrol Jul 18, 2023
8fcb465
bump-version will use dev in multiqc_config.yml if the new version is…
mirpedrol Jul 18, 2023
19a19f6
remove last / from bump-version pattern
mirpedrol Jul 18, 2023
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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 @@ -4,6 +4,7 @@

### Template

- Fix links in `multiqc_config.yml` ([#2372](https://github.com/nf-core/tools/pull/2372))
- Remove default false from nextflow_schema.json ([#2376](https://github.com/nf-core/tools/pull/2376))
- Add module MULTIQC to modules.config ([#2377](https://github.com/nf-core/tools/pull/2377))

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9 changes: 7 additions & 2 deletions nf_core/bump_version.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,14 +45,19 @@ def bump_pipeline_version(pipeline_obj, new_version):
],
)
# multiqc_config.yaml
multiqc_new_version = "dev" if "dev" in new_version else new_version
update_file_version(
Path("assets", "multiqc_config.yml"),
pipeline_obj,
[
(
"/dev",
f"/{multiqc_new_version}",
),
(
rf"{re.escape(current_version)}",
f"{new_version}",
)
f"{multiqc_new_version}",
),
],
)

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5 changes: 3 additions & 2 deletions nf_core/lint/multiqc_config.py
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Expand Up @@ -72,12 +72,13 @@ def multiqc_config(self):
# Check that the minimum plugins exist and are coming first in the summary
try:
version = self.nf_config.get("manifest.version", "").strip(" '\"")
version = "dev" if "dev" in version else version
if "report_comment" not in mqc_yml:
raise AssertionError()
if mqc_yml["report_comment"].strip() != (
f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/{version}" '
f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/tree/{version}" '
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@SusiJo SusiJo Jul 18, 2023 •
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Comment on line 74:
What about checking if the 'manifest.version' contains the 'dev' tag? Then it would also be possible to refer to the dev version of the pipeline and documentation and wouldn't create a false link.

if ("dev" in version):
    version = "dev"

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good idea, thanks for the suggestion! I have pushed the changes :)

f'target="_blank">nf-core/{self.pipeline_name}</a> analysis pipeline. For information about how to '
f'interpret these results, please see the <a href="https://nf-co.re/{self.pipeline_name}/{version}/output" '
f'interpret these results, please see the <a href="https://nf-co.re/{self.pipeline_name}/{version}/docs/output" '
'target="_blank">documentation</a>.'
):
raise AssertionError()
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10 changes: 8 additions & 2 deletions nf_core/pipeline-template/assets/multiqc_config.yml
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@@ -1,7 +1,13 @@
report_comment: >
This report has been generated by the <a href="https://github.com/{{ name }}/{{ version}}" target="_blank">{{ name }}</a>
{% if 'dev' in version -%}
This report has been generated by the <a href="https://github.com/{{ name }}/tree/dev" target="_blank">{{ name }}</a>
analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
<a href="https://nf-co.re/{{ short_name }}/{{ version }}/output" target="_blank">documentation</a>.{% endif %}
<a href="https://nf-co.re/{{ short_name }}/dev/docs/output" target="_blank">documentation</a>.{% endif %}
{%- else %}
This report has been generated by the <a href="https://github.com/{{ name }}/tree/{{ version }}" target="_blank">{{ name }}</a>
analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
<a href="https://nf-co.re/{{ short_name }}/{{ version }}/docs/output" target="_blank">documentation</a>.{% endif %}
{% endif %}
report_section_order:
"{{ name_noslash }}-methods-description":
order: -1000
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