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Added reload to {{ stage_name }}.qmd #40

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Nov 4, 2024
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pre-commit autofixes
tschwarzl authored and github-actions[bot] committed Oct 25, 2024
commit 8aa245d36952fdd437b05df0fec87eb556107dc4
12 changes: 6 additions & 6 deletions src/dso/templates/stage/quarto/src/{{ stage_name }}.qmd
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
---
title: "{{ stage_name }}"
description: "{{ stage_description }}"
description: "{{ stage_description }}"
---

# Setup
@@ -19,7 +19,7 @@ require(dso)
```{r}
#| label: read_params

# Load the stage-specific 'params.yaml' config using the `read_params(..)` function.
# Load the stage-specific 'params.yaml' config using the `read_params(..)` function.
# This function specifically loads only the stage-dependent parameters that are defined
# in the 'params', 'deps' and 'outs' section of the 'dvc.yaml' file.

@@ -28,7 +28,7 @@ params <- read_params("{{ stage_path }}")

<!--
When modifying the 'dvc.yaml', 'params.in.yaml', or 'params.yaml' files during development,
use the 'reload(params)' function in the console to ensure proper application of the changes
use the 'reload(params)' function in the console to ensure proper application of the changes
by rebuilding and reloading the configuration.
-->

@@ -37,9 +37,9 @@ by rebuilding and reloading the configuration.
```{r}
#| label: obtain_files_relative_to_stage_dir

# To locate your files relative to the stage path use `stage_here(..)`.
# e.g. when samplesheet is defined with `samplesheet = !path input/samplesheet.csv` in
# params.in.yaml and `samplesheet` is listed in 'deps' in 'dvc.yaml'
# To locate your files relative to the stage path use `stage_here(..)`.
# e.g. when samplesheet is defined with `samplesheet = !path input/samplesheet.csv` in
# params.in.yaml and `samplesheet` is listed in 'deps' in 'dvc.yaml'

samplesheet <- readr::read_csv(stage_here(params$samplesheet))
```