From ba826b936d2fd1783e0564e7b02d8c8138418aa3 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 27 Feb 2024 11:51:27 -0600 Subject: [PATCH 1/4] feat: Add config profile contact github and email https://github.com/nf-core/configs/issues/580 --- nf_core/pipeline-template/nextflow.config | 2 ++ nf_core/pipeline-template/nextflow_schema.json | 16 +++++++++++++++- 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 17e75f18a4..d2fd8039b9 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -47,6 +47,8 @@ params { custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null + config_profile_contact_github = null + config_profile_contact_email = null config_profile_url = null {%- endif %} diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 77b1a7a070..a65dffd61d 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -112,10 +112,24 @@ }, "config_profile_contact": { "type": "string", - "description": "Institutional config contact information.", + "description": "Institutional config contact name.", "hidden": true, "fa_icon": "fas fa-users-cog" }, + "config_profile_contact": { + "type": "string", + "description": "Institutional config contact GitHub username.", + "hidden": true, + "fa_icon": "fas fa-github-alt" + "pattern": "^@([A-Za-z0-9_]+)$" + }, + "config_profile_contact_email ": { + "type": "string", + "description": "Email address for the institutional config contact.", + "hidden": true, + "fa_icon": "fas fa-envelope", + "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" + }, "config_profile_url": { "type": "string", "description": "Institutional config URL link.", From 6914c42492afe009934382577a549ebefe5a6fea Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 27 Feb 2024 11:53:26 -0600 Subject: [PATCH 2/4] style: Align all params by ='s Could also do it by section but currently it was just chaos --- nf_core/pipeline-template/nextflow.config | 60 +++++++++++------------ 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index d2fd8039b9..87513099ba 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -11,52 +11,52 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options - input = null + input = null {%- if igenomes %} // References - genome = null - igenomes_base = 's3://ngi-igenomes/igenomes/' - igenomes_ignore = false - fasta = null + genome = null + igenomes_base = 's3://ngi-igenomes/igenomes/' + igenomes_ignore = false + fasta = null {%- endif -%} // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' - multiqc_methods_description = null + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' + multiqc_methods_description = null // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - version = false + outdir = null + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = null + help = false + version = false // Config options - config_profile_name = null - config_profile_description = null + config_profile_name = null + config_profile_description = null {%- if nf_core_configs %} - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_contact = null - config_profile_contact_github = null - config_profile_contact_email = null - config_profile_url = null + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_contact = null + config_profile_contact_github = null + config_profile_contact_email = null + config_profile_url = null {%- endif %} // Max resource options // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' + max_memory = '128.GB' + max_cpus = 16 + max_time = '240.h' // Schema validation default options validationFailUnrecognisedParams = false From 1619827302d0376f3a79eadfc392fa8899cb440b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 27 Feb 2024 17:55:28 +0000 Subject: [PATCH 3/4] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3fe084d81a..a1cf9af04d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -118,6 +118,8 @@ - Update actions/cache action to v4 ([#2666](https://github.com/nf-core/tools/pull/2666)) - Update peter-evans/create-or-update-comment action to v4 ([#2683](https://github.com/nf-core/tools/pull/2683)) - Update peter-evans/create-or-update-comment action to v4 ([#2695](https://github.com/nf-core/tools/pull/2695)) +- Set pdiff as nf-test differ in Docker image for Gitpod ([#2642](https://github.com/nf-core/tools/pull/2642)) +- Add config contacts ([#2800](https://github.com/nf-core/tools/pull/2800)) ## [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20] From 91023573e041afcb6524353c181a117d4f116fc7 Mon Sep 17 00:00:00 2001 From: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Date: Tue, 5 Mar 2024 12:20:47 -0600 Subject: [PATCH 4/4] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- nf_core/pipeline-template/nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index a65dffd61d..5a6eb1b61e 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -116,11 +116,11 @@ "hidden": true, "fa_icon": "fas fa-users-cog" }, - "config_profile_contact": { + "config_profile_contact_github": { "type": "string", "description": "Institutional config contact GitHub username.", "hidden": true, - "fa_icon": "fas fa-github-alt" + "fa_icon": "fas fa-github-alt", "pattern": "^@([A-Za-z0-9_]+)$" }, "config_profile_contact_email ": {