https://github.com/juke34/daisy-chaining-aline
Example of daisy chaining nextflow pipeline with the AliNe pipeline
https://github.com/juke34/daisy-chaining-aline
cascade daisy-chain nextflow
Last synced: 4 months ago
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Example of daisy chaining nextflow pipeline with the AliNe pipeline
- Host: GitHub
- URL: https://github.com/juke34/daisy-chaining-aline
- Owner: Juke34
- License: mit
- Created: 2025-02-03T14:48:24.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-03T20:37:08.000Z (over 1 year ago)
- Last Synced: 2025-10-06T22:59:33.316Z (8 months ago)
- Topics: cascade, daisy-chain, nextflow
- Language: Nextflow
- Homepage:
- Size: 71.3 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
Daisy chaining AliNe
=========================================
This repository provides an example of how to integrate an external Nextflow pipeline, such as [AliNe](https://github.com/Juke34/AliNe), into another pipeline seamlessly.
* [Foreword](#foreword)
* [Installation](#installation)
* [Nextflow](#nextflow)
* [Container platform](#container-platform)
* [Docker](#docker)
* [Singularity](#singularity)
* [Usage and test](#usage)
## Foreword
The example pipeline, daisy-chaining-aline, consists of two steps. The first step calls AliNe and retrieves the sorted BAM file it generates. The second step represents the continuation of the pipeline—here, for simplicity, it runs samtools stats as a demonstration.
AliNe is a Nextflow-based pipeline designed for efficient read alignment against a reference genome using various alignment tools of your choice. For more details, visit the [AliNe repository](https://github.com/Juke34/AliNe).
## Installation
The prerequisites to run the pipeline are:
* [Nextflow](https://www.nextflow.io/) >= 22.04.0
* [Docker](https://www.docker.com) or [Singularity](https://sylabs.io/singularity/)
### Nextflow
* Via conda
See here
```bash
conda create -n nextflow
conda activate nextflow
conda install bioconda::nextflow
```
* Manually
See here
Nextflow runs on most POSIX systems (Linux, macOS, etc) and can typically be installed by running these commands:
```bash
# Make sure 11 or later is installed on your computer by using the command:
java -version
# Install Nextflow by entering this command in your terminal(it creates a file nextflow in the current dir):
curl -s https://get.nextflow.io | bash
# Add Nextflow binary to your user's PATH:
mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin
```
### Container platform
To run the workflow you will need a container platform: docker or singularity.
### Docker
Please follow the instructions at the [Docker website](https://docs.docker.com/desktop/)
### Singularity
Please follow the instructions at the [Singularity website](https://docs.sylabs.io/guides/latest/admin-guide/installation.html)
## Usage
### Help
You can first check the available options and parameters by running:
```bash
nextflow run Juke34/daisy-chaining-aline -r v1.0.0 --help
```
### Profile
To run the workflow you must select a profile according to the container platform you want to use:
- `singularity`, a profile using Singularity to run the containers
- `docker`, a profile using Docker to run the containers
The command will look like that:
```bash
nextflow run Juke34/daisy-chaining-aline -r v1.0.0 -profile docker
```
### Example
A typical command might look like the following.
Here, we use the docker container platform, remote read and genome files, specify that we use single-ended short reads, list a number of aligners, enable trimming with fastp and provide specific options for the star aligner.
```bash
nextflow run Juke34/daisy-chaining-aline \
-r v1.0.0 \
-profile docker \
--reads https://github.com/Juke34/AliNe/raw/refs/heads/main/test/illumina/yeast_R1.fastq.gz,https://github.com/Juke34/AliNe/raw/refs/heads/main/test/illumina/yeast_R2.fastq.gz \
--genome https://raw.githubusercontent.com/Juke34/AliNe/refs/heads/main/test/yeast.fa \
--read_type short_single \
--aligner hisat2,bowtie2
```