5b1018434e
Build pipeline: vsh-ci-template-8vdc6
Source commit: 861319f5dd
Source message: Merge pull request #4 from viash-hub/update-star-align-params
update param
84 lines
2.4 KiB
Plaintext
84 lines
2.4 KiB
Plaintext
---
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format: gfm
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---
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```{r setup, include=FALSE}
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project <- yaml::read_yaml("_viash.yaml")
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```
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# 🛝📦 `r project$name`
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[](`r project$links$repository`)
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[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", project$viash_version)`-blue)](https://viash.io)
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`r project$description`
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## Quickstart
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### Requirements
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To run the components and workflows included in this repository, you need to have the following software installed:
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* Bash (>= 3.2) or an equivalent shell
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* Java Development Kit (>= 12)
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* Docker
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* Viash (>= 0.6.7)
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* Nextflow (>= 21.04)
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### Cloning the repository
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To clone this repository to your local machine, copy the URL of the forked repository by clicking the green "Code" button and selecting HTTPS or SSH.
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In your terminal or command prompt, navigate to the directory where you want to clone the repository and enter the following command:
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```{bash}
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#| eval: false
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git clone <copied_url> playground
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cd playground
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```
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### Test dataset
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You will also need to download the test resources by running the following command.
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From the repository root, run:
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```{bash}
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#| eval: false
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./test_data.sh
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```
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This will create the `test_data` folder and a file called `params_file.yaml`; the latter can be
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used to run the worklow with the generated test data.
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### Building
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Before running the workflow, the viash components need to be build and the docker images generated.
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```{bash}
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#| eval: false
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viash ns build --parallel --setup cachedbuild
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```
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::: {.callout-note}
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The `--setup cachedbuild` enables building the docker images.
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:::
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You will now see a `target` folder inside the root of the repository.
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### Testing the workflow
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To use the workflow with test data, use the following command (from the root of the repository):
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```{bash}
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#| eval: false
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nextflow run . -main-script ./target/nextflow/mapping_and_qc/main.nf \
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-params-file ./params_file.yaml \
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-profile docker \
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-c ./target/nextflow/mapping_and_qc/nextflow.config
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```
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The output will be written to the folder `test_run_output`, as specified in the `publish_dir` argument
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in the `params_file.yaml`.
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## Support and Community
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For support, questions, or to join our community:
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- **Issues**: Submit questions or issues via the [GitHub issue tracker](`r project$links$issue_tracker`).
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- **Discussions**: Join our discussions via [GitHub Discussions](`r project$links$repository`/discussions). |