From d0a8ea26f321fb8d3b2f0825e4a34b3d8c92948a Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Sun, 26 Oct 2025 11:55:29 +0100 Subject: [PATCH 1/5] feat: added profiles directory with a README.txt --- profiles/README.txt | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 profiles/README.txt diff --git a/profiles/README.txt b/profiles/README.txt new file mode 100644 index 0000000..ce7b18c --- /dev/null +++ b/profiles/README.txt @@ -0,0 +1,9 @@ +A 'profiles' directory might contain workflow resource configuration for a particular cluster or cloud instance. + +We encourage to include a profile for your use case as: + +`profiles//config.yaml` + +You may include a readme file next to the config.yaml file to point out pitfalls or other things to consider. + +Feel free to open pull requests for 3rd party workflows you are working with to include such a profile! It might also be necessary to occasionally label certain rules of a particular workflow with the `localrules: , , ...` directive when workflow developers focussed on server execution during development, e.g. plotting and dowload rules. From a1b6b495aaeb340a990f52a2d4d3e5440e2f6a67 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Sun, 26 Oct 2025 12:00:42 +0100 Subject: [PATCH 2/5] feat: included information to the profiles directory --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index 34d90f8..d428929 100644 --- a/README.md +++ b/README.md @@ -50,6 +50,14 @@ Run the workflow with: snakemake --cores 2 --sdm conda apptainer --directory .test ``` +## The "profiles" Directory + +When developing on a cluster or cloud instance, please include a "profiles" directory: + +`profiles//config.yaml` + +This configuration file should contain the workflow profile with its resource specification for a particular execution environment (cluster or cload). You may include a readme file next to point out pitfalls or other aspects worth a user's consideration. + ## Authors - Firstname Lastname From 73e9dc28a982254d821a707a17f928ba63f9e369 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Sun, 26 Oct 2025 12:09:26 +0100 Subject: [PATCH 3/5] Update profiles/README.txt Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --- profiles/README.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/profiles/README.txt b/profiles/README.txt index ce7b18c..5bbe6e1 100644 --- a/profiles/README.txt +++ b/profiles/README.txt @@ -6,4 +6,4 @@ We encourage to include a profile for your use case as: You may include a readme file next to the config.yaml file to point out pitfalls or other things to consider. -Feel free to open pull requests for 3rd party workflows you are working with to include such a profile! It might also be necessary to occasionally label certain rules of a particular workflow with the `localrules: , , ...` directive when workflow developers focussed on server execution during development, e.g. plotting and dowload rules. +We welcome pull requests for 3rd-party workflows you are working with to include such a profile! It may also be necessary to occasionally label certain rules of a particular workflow with the `localrules: , , ...` directive when workflow developers focused on server execution during development, e.g., plotting and download rules. From 04f13c0fbe60d32ed96493bb7d1aecfe03c0c0cf Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Sun, 26 Oct 2025 12:09:52 +0100 Subject: [PATCH 4/5] Update README.md Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d428929..a138152 100644 --- a/README.md +++ b/README.md @@ -56,7 +56,7 @@ When developing on a cluster or cloud instance, please include a "profiles" dire `profiles//config.yaml` -This configuration file should contain the workflow profile with its resource specification for a particular execution environment (cluster or cload). You may include a readme file next to point out pitfalls or other aspects worth a user's consideration. +This configuration file should contain the workflow profile with its resource specification for a particular execution environment (cluster or cloud). You may include a readme file next to point out pitfalls or other aspects worth a user's consideration. ## Authors From 014867f449ec6c00cad16850a827ef0df026eb50 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Sun, 26 Oct 2025 12:26:18 +0100 Subject: [PATCH 5/5] fix: added missing content section --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index a138152..6a6ba38 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,7 @@ A Snakemake workflow for `` - [Snakemake workflow: ``](#snakemake-workflow-name) - [Usage](#usage) - [Deployment options](#deployment-options) + - [The "profiles" Directory](#the-profiles-directory) - [Authors](#authors) - [References](#references) - [TODO](#todo)