A set of scripts for Nextflow demo purpose.
- Java 7 or 8
- Docker engine 1.10.x (or higher)
Install Nextflow by using the following command:
curl -fsSL get.nextflow.io | bash
Then copy the script nextflow in a directory on your PATH.
Finally, clone this repository with the following command:
git clone https://github.com/nextflow-io/demo.git nextflow-demo && cd nextflow-demo
The first example run a very simple two-steps pipeline which execute a protein sequence alignment and the create a phylogenetic tree. To run this example enter the following command in your shell terminal:
nextflow run demo.nf
The tree output file is written in the results directory.
By default the script uses the sequences FASTA file named data/BB11001.tfa. To use
a different input file specify the --seq command line option as shown below:
nextflow run demo.nf --seq data/BB11029.tfa
Check the output in the results folder as before.
In order to run the same script against multiple input sequences specify the input by using the common Linux wildcards. For example:
nextflow run demo.nf --seq 'data/BB11*'
Note: make sure to wrap the input parameter in quote characters as shown above, to avoid that BASH expand the star wildcard to the actual file names.
The following example shows how to execute multiple alignments and create a single phylogenetic tree from all of them.
nextflow run demo2.nf --seq 'data/BB11*'