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zarp

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The Zavolab Automated RNA-seq Pipeline

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**ZARP** ([Zavolab][zavolan-lab] Automated RNA-seq Pipeline) is a generic RNA-Seq analysis workflow that allows users to process and analyze Illumina short-read sequencing libraries with minimum effort. Better yet: With our companion [**ZARP-cli**](https://github.com/zavolanlab/zarp-cli) command line interface, you can start ZARP runs with the simplest and most intuitive commands.

_RNA-seq analysis doesn't get simpler than that!_

The workflow is developed in [Snakemake][snakemake], a widely used workflow management system in the bioinformatics community. ZARP will pre-process, align and quantify your single- or paired-end stranded bulk RNA-seq sequencing libraries with publicly available state-of-the-art bioinformatics tools. ZARP's browser-based rich reports and visualizations will give you meaningful initial insights in the quality and composition of your sequencing experiments - fast and simple. Whether you are an experimentalist struggling with large scale data analysis or an experienced bioinformatician, when there's RNA-seq data to analyze, just _zarp 'em_!

# Documentation

For the full documentation please visit the [ZARP website](https://zavolanlab.github.io/zarp).

# Quick installation

> **IMPORTANT: Rather than installing the ZARP workflow as described in this section, we
> recommend installing [ZARP-cli](https://github.com/zavolanlab/zarp-cli) for most use
> cases!** If you follow its [installation
> instructions](https://zavolanlab.github.io/zarp-cli/guides/installation/), you can
> skip the instructions below.

Quick installation requires the following:
- Linux
- Git
- [Conda][conda] >= 24.11.3
- Optional: [Apptainer][apptainer] >=1.3.6  (required only if you want to use containers to manage 
  tool environments)

```bash
git clone https://github.com/zavolanlab/zarp.git
cd zarp
conda env create -f install/environment.yml
conda activate zarp
```

# Basic usage

You can trigger ZARP without ZARP-cli. This is convenient for users who have some experience with Snakemake and don't want to use a CLI to trigger their runs. Extensive documentation of the usage is available in the [usage documentation](https://zavolanlab.github.io/zarp/guides/usage/), while below you can find the basic steps to trigger a run.

1. Assuming that your current directory is the workflow repository's root directory,
create a directory for your workflow run and move into it with:

```bash
    mkdir config/my_run
    cd config/my_run
    ```

2. Create an empty sample table and a workflow configuration file:

```bash
    touch samples.tsv
    touch config.yaml
    ```

3. Use your editor of choice to populate these files with appropriate
values. Have a look at the examples in the `tests/` directory to see what the
files should look like, specifically:

- [samples.tsv](https://github.com/zavolanlab/zarp/blob/dev/tests/input_files/samples.tsv)
    - [config.yaml](https://github.com/zavolanlab/zarp/blob/dev/tests/input_files/config.yaml)

4. Create a runner script. Pick one of the following choices for either local
or cluster execution. Before execution of the respective command, you need to
remember to update the argument of the `--apptainer-args` option of a
respective profile (file: `profiles/{profile}/config.yaml`) so that
it contains a comma-separated list of _all_ directories
containing input data files (samples and any annotation files etc) required for
your run.

Runner script for _local execution_:

```bash
    cat << "EOF" > run.sh
    #!/bin/bash

snakemake \
        --profile="../../profiles/local-apptainer" \
        --configfile="config.yaml"

EOF
    ```

**OR**

Runner script for _Slurm cluster execution_ (note that you may need
    to modify the arguments to `--jobs` and `--cores` in the file:
    `profiles/slurm-apptainer/config.yaml` depending on your HPC
    and workload manager configuration):

```bash
    cat << "EOF" > run.sh
    #!/bin/bash
    mkdir -p logs/cluster_log
    snakemake \
        --profile="../profiles/slurm-apptainer" \
        --configfile="config.yaml"
    EOF
    ```

> Note: When running the pipeline with *Conda* you should use `local-conda` and
    `slurm-conda` profiles instead.

> Note: The slurm profiles are adapted to a cluster that uses the quality-of-service (QOS) keyword. If QOS is not supported by your slurm instance, you have to remove all the lines with "qos" in `profiles/slurm-config.json`.

5. Start your workflow run:

```bash
    bash run.sh
    ```

## Contributing

This project lives off your contributions, be it in the form of bug reports,
feature requests, discussions, or fixes and other code changes. Please refer
to the [contributing guidelines](CONTRIBUTING.md) if you are interested to
contribute. Please mind the [code of conduct](CODE_OF_CONDUCT.md) for all
interactions with the community.

## Contact

For questions or suggestions regarding the code, please use the
[issue tracker][issue-tracker]. For any other inquiries, please contact us
by [email][contact].

[conda]: <https://docs.conda.io/projects/conda/en/latest/index.html>
[hts-infer]: <https://github.com/zavolanlab/htsinfer>
[profiles]: <https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles>
[miniconda-installation]: <https://docs.conda.io/en/latest/miniconda.html>
[rule-graph]: images/rule_graph.svg
[zarp-logo]: images/zarp_logo.svg
[zarp-schema]: images/zarp_schema.svg
[sample-doc]: pipeline_documentation.md#read-sample-table
[snakemake]: <https://snakemake.readthedocs.io/en/stable/>
[apptainer]: <https://apptainer.org/>
[apptainer-install]: <https://apptainer.org/documentation/>
[slurm]: <https://slurm.schedmd.com/documentation.html>
[zavolan-lab]: <https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/>
[pipeline-documentation]: pipeline_documentation.md
[resources.tmpdir]: <https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html?#standard-resources>
[zavolab]: <https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/>
[contact]: <mailto:zavolab-biozentrum@unibas.ch>

zarp

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