Using Nextflow in Galaxy

gistfile1.txt

# Using Nextflow in Galaxy

* Nextflow is the workflow management tool used widely in bioinformatics
* Galaxy is a server based GUI tool with a nice interface and is also used to start workflows

## Can it be done ? 

* There are few reports online, but it is possible. eg https://galaxyproject.org/blog/2022-08-15-making-nextflow-work-with-galaxy-at-cfsan-fda/
* The main requirements: 
* a) install Nextflow using a direct JAR download, not via conda. This may be because it collides with the internal Galaxy conda environments
* b) Output files directly to the Galaxy tool output dir directory. 

An install script for getting the nextflow.jar file

```
#!/bin/bash
source /etc/profile

set -e

# Download nextflow jar directly - no conda needed
wget -q -c -nc https://github.com/nextflow-io/nextflow/releases/download/v23.04.2/nextflow-23.04.2-all
mv nextflow-23.04.2-all nextflow
chmod a+x nextflow*

echo Done
```

Then if you use a shell script to start your nextflow tool, you need to set up a system Java installation and tell bash where to find it.
This is just an example 


run.sh script
```
#!/bin/bash
set -e

# Setup java env - in MO for omics user
unset JAVA_HOME
unset _JAVA_OPTIONS
unset JAVA_OPTIONS
export JAVA_HOME=/path/to/software/java/jdk/jdk-16/

# Run nextflow - note that nextflow is a self contained ca 95 MB JAR file

 /path/to/nextflow run pipelein.nf -dsl2 -c $src/src/nextflow_large.config --ref_fasta $ref --outdir $output -with-timeline -with-report -with-dag EDTA_flowchart.dot -resume

```



Now you should be able to set up Galaxy using the tool xml to run the `run.sh` script here.