From 7931c7f658712e15d522531616c3e001849e338b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 20 Aug 2024 12:43:06 +0200 Subject: [PATCH 1/4] add option to exclude license from pipeline template --- nf_core/pipelines/create/templatefeatures.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index b97bf347a..dc3f07271 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -242,3 +242,18 @@ changelog: - "CHANGELOG.md" nfcore_pipelines: False custom_pipelines: True +license: + skippable_paths: + - "LICENSE" + short_description: "Add a license" + description: "Add the MIT license file." + help_text: | + To protect the copyright of the pipeline, you can add a LICENSE file. + This option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT + linting: + files_exist: + - "LICENSE" + files_unchanged: + - "LICENSE" + nfcore_pipelines: False + custom_pipelines: True From 6ff0929c0956b148839c231133b440f5f0cd876a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 20 Aug 2024 10:46:47 +0000 Subject: [PATCH 2/4] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a450a672..b530f597b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108)) - add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112)) +- add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) ### Linting From 78d469fd893a6e1c45aa59330378f213a994fdbf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 20 Aug 2024 12:56:04 +0200 Subject: [PATCH 3/4] Update nf_core/pipelines/create/templatefeatures.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/templatefeatures.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index dc3f07271..a8a6ce565 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -245,7 +245,7 @@ changelog: license: skippable_paths: - "LICENSE" - short_description: "Add a license" + short_description: "Add a license File" description: "Add the MIT license file." help_text: | To protect the copyright of the pipeline, you can add a LICENSE file. From 34565c1e12ce20cda823e4e92eed6c084501821f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 20 Aug 2024 13:00:04 +0200 Subject: [PATCH 4/4] update textual snapshots --- .../__snapshots__/test_create_app.ambr | 512 +++++++++--------- 1 file changed, 256 insertions(+), 256 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr index f4eb25508..66c08faba 100644 --- a/tests/pipelines/__snapshots__/test_create_app.ambr +++ b/tests/pipelines/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-3220763577-matrix { + .terminal-2278814444-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3220763577-title { + .terminal-2278814444-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3220763577-r1 { fill: #c5c8c6 } - .terminal-3220763577-r2 { fill: #e3e3e3 } - .terminal-3220763577-r3 { fill: #989898 } - .terminal-3220763577-r4 { fill: #e1e1e1 } - .terminal-3220763577-r5 { fill: #4ebf71;font-weight: bold } - .terminal-3220763577-r6 { fill: #1e1e1e } - .terminal-3220763577-r7 { fill: #507bb3 } - .terminal-3220763577-r8 { fill: #e2e2e2 } - .terminal-3220763577-r9 { fill: #808080 } - .terminal-3220763577-r10 { fill: #dde6ed;font-weight: bold } - .terminal-3220763577-r11 { fill: #001541 } - .terminal-3220763577-r12 { fill: #0178d4 } - .terminal-3220763577-r13 { fill: #454a50 } - .terminal-3220763577-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-3220763577-r15 { fill: #000000 } - .terminal-3220763577-r16 { fill: #e4e4e4 } - .terminal-3220763577-r17 { fill: #14191f } - .terminal-3220763577-r18 { fill: #7ae998 } - .terminal-3220763577-r19 { fill: #0a180e;font-weight: bold } - .terminal-3220763577-r20 { fill: #008139 } - .terminal-3220763577-r21 { fill: #fea62b;font-weight: bold } - .terminal-3220763577-r22 { fill: #a7a9ab } - .terminal-3220763577-r23 { fill: #e2e3e3 } + .terminal-2278814444-r1 { fill: #c5c8c6 } + .terminal-2278814444-r2 { fill: #e3e3e3 } + .terminal-2278814444-r3 { fill: #989898 } + .terminal-2278814444-r4 { fill: #e1e1e1 } + .terminal-2278814444-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2278814444-r6 { fill: #1e1e1e } + .terminal-2278814444-r7 { fill: #507bb3 } + .terminal-2278814444-r8 { fill: #e2e2e2 } + .terminal-2278814444-r9 { fill: #808080 } + .terminal-2278814444-r10 { fill: #dde6ed;font-weight: bold } + .terminal-2278814444-r11 { fill: #001541 } + .terminal-2278814444-r12 { fill: #0178d4 } + .terminal-2278814444-r13 { fill: #454a50 } + .terminal-2278814444-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-2278814444-r15 { fill: #000000 } + .terminal-2278814444-r16 { fill: #e4e4e4 } + .terminal-2278814444-r17 { fill: #14191f } + .terminal-2278814444-r18 { fill: #7ae998 } + .terminal-2278814444-r19 { fill: #0a180e;font-weight: bold } + .terminal-2278814444-r20 { fill: #008139 } + .terminal-2278814444-r21 { fill: #fea62b;font-weight: bold } + .terminal-2278814444-r22 { fill: #a7a9ab } + .terminal-2278814444-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Hide help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common reference  - genome files.▂▂ - - By selecting this option, your pipeline will include a configuration file  - specifying the paths to these files. - - The required code to use these files will also be included in the template.  - When the pipeline user provides an appropriate genome key, the pipeline will - automatically download the required reference files. - ▅▅ - For more information about reference genomes in nf-core pipelines, see the  - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Hide help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common reference  + genome files. + + By selecting this option, your pipeline will include a configuration file  + specifying the paths to these files. + + The required code to use these files will also be included in the template.  + When the pipeline user provides an appropriate genome key, the pipeline will + automatically download the required reference files. + ▅▅ + For more information about reference genomes in nf-core pipelines, see the  + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-537214554-matrix { + .terminal-2282176583-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-537214554-title { + .terminal-2282176583-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-537214554-r1 { fill: #c5c8c6 } - .terminal-537214554-r2 { fill: #e3e3e3 } - .terminal-537214554-r3 { fill: #989898 } - .terminal-537214554-r4 { fill: #e1e1e1 } - .terminal-537214554-r5 { fill: #4ebf71;font-weight: bold } - .terminal-537214554-r6 { fill: #1e1e1e } - .terminal-537214554-r7 { fill: #507bb3 } - .terminal-537214554-r8 { fill: #e2e2e2 } - .terminal-537214554-r9 { fill: #808080 } - .terminal-537214554-r10 { fill: #dde6ed;font-weight: bold } - .terminal-537214554-r11 { fill: #001541 } - .terminal-537214554-r12 { fill: #14191f } - .terminal-537214554-r13 { fill: #454a50 } - .terminal-537214554-r14 { fill: #7ae998 } - .terminal-537214554-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-537214554-r16 { fill: #0a180e;font-weight: bold } - .terminal-537214554-r17 { fill: #000000 } - .terminal-537214554-r18 { fill: #008139 } - .terminal-537214554-r19 { fill: #fea62b;font-weight: bold } - .terminal-537214554-r20 { fill: #a7a9ab } - .terminal-537214554-r21 { fill: #e2e3e3 } + .terminal-2282176583-r1 { fill: #c5c8c6 } + .terminal-2282176583-r2 { fill: #e3e3e3 } + .terminal-2282176583-r3 { fill: #989898 } + .terminal-2282176583-r4 { fill: #e1e1e1 } + .terminal-2282176583-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2282176583-r6 { fill: #1e1e1e } + .terminal-2282176583-r7 { fill: #507bb3 } + .terminal-2282176583-r8 { fill: #e2e2e2 } + .terminal-2282176583-r9 { fill: #808080 } + .terminal-2282176583-r10 { fill: #dde6ed;font-weight: bold } + .terminal-2282176583-r11 { fill: #001541 } + .terminal-2282176583-r12 { fill: #14191f } + .terminal-2282176583-r13 { fill: #454a50 } + .terminal-2282176583-r14 { fill: #7ae998 } + .terminal-2282176583-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-2282176583-r16 { fill: #0a180e;font-weight: bold } + .terminal-2282176583-r17 { fill: #000000 } + .terminal-2282176583-r18 { fill: #008139 } + .terminal-2282176583-r19 { fill: #fea62b;font-weight: bold } + .terminal-2282176583-r20 { fill: #a7a9ab } + .terminal-2282176583-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help ▇▇ - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - requried to run  - nf-core pipelines at  - different institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - and CI tests to lint  - your code: pre-commit, - editor-config and  - prettier. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Include citationsInclude pipeline tools Show help  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▇▇ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + requried to run  + nf-core pipelines at  + different institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + and CI tests to lint  + your code: pre-commit, + editor-config and  + prettier. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Include citationsInclude pipeline tools Show help  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit