From f20f797ce755bdd2647bb951be37d54c2435921b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 7 Oct 2024 11:35:22 +0200 Subject: [PATCH] fix some more template newlines --- nf_core/pipeline-template/.github/CONTRIBUTING.md | 4 ++-- nf_core/pipeline-template/docs/output.md | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md index f331d3867..63cddcb7f 100644 --- a/nf_core/pipeline-template/.github/CONTRIBUTING.md +++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md @@ -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. @@ -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 diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md index 5e42d50cc..083c46ecd 100644 --- a/nf_core/pipeline-template/docs/output.md +++ b/nf_core/pipeline-template/docs/output.md @@ -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`.