From 8ae861d94b9ff9d8af5edd3d44df789c69da491a Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 14 Oct 2024 15:55:02 +0200 Subject: [PATCH 1/5] keep pipeline name in version.yml file Why going for pipeline when we have shortname? --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index adad7a6a0..2a619e2e4 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -47,7 +47,7 @@ workflow {{ short_name|upper }} { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + 'pipeline_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml', + name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + '{{ short_name }}_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } From db1687d7615b310c793a4f4e570fd08d8295b984 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 14 Oct 2024 13:56:28 +0000 Subject: [PATCH 2/5] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3a4eaa71..1ff8468cc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,8 @@ ### General +- Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223)) + ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] ### Template From 8e2d899d8d9b462d3111b2301f0e9747a60d3675 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 14 Oct 2024 15:56:40 +0200 Subject: [PATCH 3/5] Update nf_core/pipeline-template/workflows/pipeline.nf --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 2a619e2e4..dbf5f1f89 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -47,7 +47,7 @@ workflow {{ short_name|upper }} { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + '{{ short_name }}_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml', + name: {% if is_nfcore %}'nf_core_' + {% else %}{% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% else %}{% endif %} + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } From 597a0ae54acbfca5e8f0758e6856d96ae4a1385b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 14 Oct 2024 14:09:41 +0000 Subject: [PATCH 4/5] [automated] Update CHANGELOG.md --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1ff8468cc..c4da12990 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ### Template +- Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223)) + ### Download ### Linting @@ -14,8 +16,6 @@ ### General -- Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223)) - ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] ### Template From 18cbf05530d40b71546e23e146d53719d852916a Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 15 Oct 2024 09:45:40 +0200 Subject: [PATCH 5/5] Update nf_core/pipeline-template/workflows/pipeline.nf MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: JĂșlia Mir Pedrol --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index dbf5f1f89..4dd8674c1 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/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 %} '{{ short_name }}_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 }