From fa4adcb77251375a6f39532246a230f791d38842 Mon Sep 17 00:00:00 2001 From: David Laehnemann <1379875+dlaehnemann@users.noreply.github.com> Date: Wed, 14 Jan 2026 13:25:37 +0100 Subject: [PATCH 1/3] docs: add info on `profiles/` deployment to workflow_deployment.rst --- docs/workflow_users/workflow_deployment.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/workflow_users/workflow_deployment.rst b/docs/workflow_users/workflow_deployment.rst index f346bde..e62e68d 100644 --- a/docs/workflow_users/workflow_deployment.rst +++ b/docs/workflow_users/workflow_deployment.rst @@ -35,8 +35,8 @@ For the example above, it will have the following content use rule * from dna_seq_varlociraptor utilizing `Snakemake's module system `__. -In addition, it will copy over the contents of the ``config`` directory of the given repository into ``/tmp/dest/workflow/Snakefile``. -These should be seen as a template, can be modified according to your needs. +In addition, it will copy over the ``config/`` and ``profiles/`` directories of the given repository (and their contents) into respective directories under``/tmp/dest/``. +These should be seen as a template, and can be modified according to your needs. Further, the workflow definition Snakefile can be arbitrarily extended and modified, thereby making any changes to the used workflow transparent (also see the `snakemake module documentation `_). It is highly advisable to put the deployed workflow into a new (perhaps private) git repository (e.g., see `here `_ for instructions how to do that with Github). From db15af631a50d6c7b3b660b57393a466e7e051cc Mon Sep 17 00:00:00 2001 From: David Laehnemann <1379875+dlaehnemann@users.noreply.github.com> Date: Wed, 14 Jan 2026 14:03:55 +0100 Subject: [PATCH 2/3] docs: add missing space Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --- docs/workflow_users/workflow_deployment.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/workflow_users/workflow_deployment.rst b/docs/workflow_users/workflow_deployment.rst index e62e68d..e5d7738 100644 --- a/docs/workflow_users/workflow_deployment.rst +++ b/docs/workflow_users/workflow_deployment.rst @@ -35,7 +35,7 @@ For the example above, it will have the following content use rule * from dna_seq_varlociraptor utilizing `Snakemake's module system `__. -In addition, it will copy over the ``config/`` and ``profiles/`` directories of the given repository (and their contents) into respective directories under``/tmp/dest/``. +In addition, it will copy over the ``config/`` and ``profiles/`` directories of the given repository (and their contents) into respective directories under ``/tmp/dest/``. These should be seen as a template, and can be modified according to your needs. Further, the workflow definition Snakefile can be arbitrarily extended and modified, thereby making any changes to the used workflow transparent (also see the `snakemake module documentation `_). From 3f80eb396a856eee0c5a9fed3fec4a9adc849973 Mon Sep 17 00:00:00 2001 From: David Laehnemann <1379875+dlaehnemann@users.noreply.github.com> Date: Wed, 14 Jan 2026 14:05:01 +0100 Subject: [PATCH 3/3] docs: correct grammar of modified sentence Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --- docs/workflow_users/workflow_deployment.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/workflow_users/workflow_deployment.rst b/docs/workflow_users/workflow_deployment.rst index e5d7738..18b8f27 100644 --- a/docs/workflow_users/workflow_deployment.rst +++ b/docs/workflow_users/workflow_deployment.rst @@ -36,7 +36,7 @@ For the example above, it will have the following content utilizing `Snakemake's module system `__. In addition, it will copy over the ``config/`` and ``profiles/`` directories of the given repository (and their contents) into respective directories under ``/tmp/dest/``. -These should be seen as a template, and can be modified according to your needs. +These should be seen as templates, and can be modified according to your needs. Further, the workflow definition Snakefile can be arbitrarily extended and modified, thereby making any changes to the used workflow transparent (also see the `snakemake module documentation `_). It is highly advisable to put the deployed workflow into a new (perhaps private) git repository (e.g., see `here `_ for instructions how to do that with Github).