Skip to content

Commit

Permalink
Merge pull request #3195 from mashehu/fix-whitespaces
Browse files Browse the repository at this point in the history
fix whitespaces in rendered template
  • Loading branch information
mirpedrol authored Oct 7, 2024
2 parents 6a2b0af + f20f797 commit 938fd34
Show file tree
Hide file tree
Showing 4 changed files with 7 additions and 6 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/sync.yml
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ jobs:
run: |
git config --global user.email "core@nf-co.re"
git config --global user.name "nf-core-bot"
nf-core --log-file sync_log_${{ matrix.pipeline }}.txt sync -d nf-core/${{ matrix.pipeline }} \
nf-core --log-file sync_log_${{ matrix.pipeline }}.txt pipelines sync -d nf-core/${{ matrix.pipeline }} \
--from-branch dev \
--pull-request \
--username nf-core-bot \
Expand Down
4 changes: 2 additions & 2 deletions nf_core/pipeline-template/.github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ You have the option to test your changes locally by running the pipeline. For re
nf-test test --profile debug,test,docker --verbose
```

{% endif %}
{% endif -%}
When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

Expand Down Expand Up @@ -95,7 +95,7 @@ If you wish to contribute a new step, please use the following coding standards:
{%- if multiqc %}
9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
{% endif %}
{%- endif %}

### Default values

Expand Down
4 changes: 2 additions & 2 deletions nf_core/pipeline-template/assets/multiqc_config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,11 @@ report_comment: >
This report has been generated by the <a href="https://github.com/{{ name }}/tree/dev" target="_blank">{{ name }}</a>
analysis pipeline.{% if is_nfcore %} For information about how to interpret these results, please see the
<a href="https://nf-co.re/{{ short_name }}/dev/docs/output" target="_blank">documentation</a>.{% endif %}
{%- else %}
{%- else -%}
This report has been generated by the <a href="https://github.com/{{ name }}/releases/tag/{{ version }}" target="_blank">{{ name }}</a>
analysis pipeline.{% if is_nfcore %} 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 %}
{%- endif %}
report_section_order:
"{{ name_noslash }}-methods-description":
order: -1000
Expand Down
3 changes: 2 additions & 1 deletion nf_core/pipeline-template/docs/output.md
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,8 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ

- `pipeline_info/`
- Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
{% if email %}- Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %}
{%- if email %}
- Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %}
- Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
- Parameters used by the pipeline run: `params.json`.

Expand Down

0 comments on commit 938fd34

Please sign in to comment.