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Update existing pipeline usage

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drpatelh 2020-08-06 12:12:40 +01:00
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README.md
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@ -26,9 +26,35 @@ The features offered by Nextflow DSL2 can be used in various ways depending on t
## Using existing modules
The Nextflow [`include`](https://www.nextflow.io/docs/edge/dsl2.html#modules-include) statement can be used within your pipelines in order to load module files that you have available locally.
We have written a helper command in the nf-core/tools package that allows you to install any module present in the `software/` directory of this repository.
You should be able to get a good idea as to how other people are using module files by looking at pipelines available in nf-core e.g. [`nf-core/chipseq`](https://github.com/nf-core/chipseq/tree/dev) (work in progress)
1. [Install](https://github.com/nf-core/tools#installation) the latest version of nf-core/tools (`>=1.10.2`)
2. List the available modules
```console
$ nf-core modules list
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 1.10.2
INFO Modules available from nf-core/modules (master): modules.py:51
bwa/index
bwa/mem
deeptools/computematrix
deeptools/plotfingerprint
deeptools/plotheatmap
deeptools/plotprofile
fastqc
..truncated..
```
### Configuration and parameters