Merge branch 'add-toggle-all-shortcut' of github.com:mashehu/tools in…

…to add-toggle-all-shortcut

CHANGELOG.md

@@ -4,6 +4,9 @@
 
 ### Template
 
+- Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223))
+- Fix Manifest DOI text ([#3224](https://github.com/nf-core/tools/pull/3224))
+
 ### Download
 
 ### Linting
@@ -15,6 +18,7 @@
 ### General
 
 - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220))
+- create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

nf_core/pipeline-template/nextflow.config

@@ -286,7 +286,7 @@ validation {
 \033[0;35m  ${manifest.name} ${manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 

nf_core/pipeline-template/workflows/pipeline.nf

@@ -47,7 +47,7 @@ workflow {{ short_name|upper }} {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + 'pipeline_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml',
+            name: {% if is_nfcore %}'nf_core_'  + {% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% endif %} + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }