CI
d6f80327e8
Build pipeline: viash-hub.biobox.update-authors-2ctwx
Source commit: 778f21dc29
Source message: add linkedin
124 lines
3.8 KiB
Plaintext
124 lines
3.8 KiB
Plaintext
---
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format: gfm
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---
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```{r setup, include=FALSE}
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package <- yaml::read_yaml("_viash.yaml")
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license <- paste0(package$links$repository, "/blob/main/LICENSE")
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contributing <- paste0(package$links$repository, "/blob/main/CONTRIBUTING.md")
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pkg <- package$name
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ver <- if (!is.null(package$version)) package$version else "v0.3.1"
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comp <- "arriba"
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```
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# 🌱📦 `r pkg`
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[](https://www.viash-hub.com/packages/`r pkg`)
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[](`r package$links$repository`)
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[](`r license`)
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[](`r package$links$issue_tracker`)
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[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", package$viash_version)`-blue.svg)](https://viash.io)
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`r package$summary`
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## Introduction
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`r package$description`
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## Example Usage
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Viash components in `r pkg` can be run in various ways:
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```{r mmd, echo=FALSE, results='asis'}
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cat(
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"```mermaid\n",
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"flowchart TD\n",
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" A[", pkg, " ", ver, "] --> B(Viash Hub Launch)\n",
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" A --> C(Viash CLI)\n",
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" A --> D(Nextflow CLI)\n",
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" A --> E(Seqera Cloud)\n",
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" A --> F(As a dependency)\n",
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"```\n",
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sep = ""
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)
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```
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### 1. Via the Viash Hub Launch interface
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You can run this component directly from the Viash Hub [Launch interface](https://www.viash-hub.com/launch?package=`r pkg`&version=`r ver`&component=`r comp`&runner=Executable).
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### 2. Via the Viash CLI
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You can run this component directly from the command line using the Viash CLI.
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```bash
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viash run vsh://`r pkg`@`r ver`/`r comp` -- --help
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viash run vsh://`r pkg`@`r ver`/`r comp` -- \
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--bam path/to/input.bam \
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--genome path/to/genome.fa \
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--gene_annotation path/to/annotation.gtf \
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--fusions path/to/output.txt
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```
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This will run the component with the specified input files and output the results to the specified output file.
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### 3. Via the Nextflow CLI or Seqera Cloud
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You can run this component as a Nextflow pipeline.
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```bash
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nextflow run https://packages.viash-hub.com/vsh/`r pkg` \
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-revision `r ver` \
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-main-script target/nextflow/`r comp`/main.nf \
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-latest -resume \
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-profile docker \
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--bam path/to/input.bam \
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--genome path/to/genome.fa \
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--gene_annotation path/to/annotation.gtf \
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--publish_dir path/to/output
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```
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**Note:** Make sure that the [Nextflow SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) is set up properly. You can do this by adding the following lines to your `~/.nextflow/scm` file:
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```groovy
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providers.vsh.platform = 'gitlab'
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providers.vsh.server = 'https://packages.viash-hub.com'
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```
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**Tip:** This will also work with Seqera Cloud or other Nextflow-compatible platforms.
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### 4. As a dependency
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In your Viash config file (`config.vsh.yaml`), you can add this component as a dependency:
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```yaml
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dependencies:
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- name: `r comp`
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repository: vsh://`r pkg`@`r ver`
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```
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**Tip:** See the [Viash documentation](https://viash.io/guide/nextflow_vdsl3/create-a-pipeline.html#pipeline-as-a-component) for more details on how to use Viash components as a dependency in your own Nextflow workflows.
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## Contributing
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Contributions are welcome! We aim to build a comprehensive collection of high-quality bioinformatics components. If you'd like to contribute, please follow these general steps:
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```{r echo=FALSE}
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lines <- readr::read_lines("CONTRIBUTING.md")
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index_start <- grep("^### Step [0-9]*:", lines)
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index_end <- c(index_start[-1] - 1, length(lines))
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name <- gsub("^### Step [0-9]*: *", "", lines[index_start])
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knitr::asis_output(
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paste(paste0(" 1. ", name, "\n"), collapse = "")
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)
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```
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See the [CONTRIBUTING](`r contributing`) file for more details.
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