diff --git a/book/workflow_frameworks/index.qmd b/book/workflow_frameworks/index.qmd index 7a0e8f9..d6eb1dc 100644 --- a/book/workflow_frameworks/index.qmd +++ b/book/workflow_frameworks/index.qmd @@ -476,100 +476,97 @@ In the following sections, we will explore the use of [Viash](https://viash.io). Use case components: -#### Bash +### Bash -:::{.grid} +Path: `src/load_data` -:::{.g-col-6} +:::{.panel-tabset} -`src/load_data/config.vsh.yaml`: +#### `config.vsh.yaml` {.unnumbered} ```{embed lang="yaml"} examples/viash_nextflow/src/load_data/config.vsh.yaml ``` -::: - -:::{.g-col-6} - -`src/load_data/script.sh`: +#### `script.sh` {.unnumbered} ```{embed lang="bash"} examples/viash_nextflow/src/load_data/script.sh ``` -::: +#### `test.sh` {.unnumbered} + +```{embed lang="bash"} +examples/viash_nextflow/src/load_data/test.sh +``` ::: -#### Python +### Python -:::{.grid} +Path: `src/subset_obs` -:::{.g-col-6} +:::{.panel-tabset} -`src/subset_obs/config.vsh.yaml`: +#### `config.vsh.yaml` {.unnumbered} ```{embed lang="yaml"} examples/viash_nextflow/src/subset_obs/config.vsh.yaml ``` -::: +#### `script.py` {.unnumbered} -:::{.g-col-6} +```{embed lang="python"} +examples/viash_nextflow/src/subset_obs/script.py +``` -`src/subset_obs/script.py`: +#### `test.py` {.unnumbered} ```{embed lang="python"} -examples/viash_nextflow/src/subset_obs/script.py +examples/viash_nextflow/src/subset_obs/test.py ``` ::: -::: +### R -#### R +Path: `src/differential_expression` -:::{.grid} - -:::{.g-col-6} +:::{.panel-tabset} -`src/differential_expression/config.vsh.yaml`: +#### `config.vsh.yaml` {.unnumbered} ```{embed lang="yaml"} examples/viash_nextflow/src/differential_expression/config.vsh.yaml ``` -::: +#### `script.R` {.unnumbered} -:::{.g-col-6} - -`src/differential_expression/script.R`: ```{embed lang="r"} examples/viash_nextflow/src/differential_expression/script.R ``` -::: +#### `test.R` {.unnumbered} + +```{embed lang="r"} +examples/viash_nextflow/src/differential_expression/test.R +``` ::: -#### Nextflow +### Nextflow -:::{.grid} +Path: `src/workflow` -:::{.g-col-6} +:::{.panel-tabset} -`src/workflow/config.vsh.yaml`: +#### `config.vsh.yaml` {.unnumbered} ```{embed lang="yaml"} examples/viash_nextflow/src/workflow/config.vsh.yaml ``` -::: - -:::{.g-col-6} - -`src/workflow/main.nf`: +#### `main.nf` {.unnumbered} ```{embed lang="groovy"} examples/viash_nextflow/src/workflow/main.nf @@ -577,8 +574,6 @@ examples/viash_nextflow/src/workflow/main.nf ::: -::: - ### Running the workflow To run the workflow, you must first build the project: @@ -634,6 +629,8 @@ nextflow run \ The workflow will process the dataset, subset the data, compute pseudobulk samples, and perform differential expression analysis. The results will be saved in the `output` directory. +### Workflow Output + ```bash tree output ```