-
Notifications
You must be signed in to change notification settings - Fork 0
/
quickstart.qmd
35 lines (24 loc) · 3.32 KB
/
quickstart.qmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
---
title: "Quickstart"
editor: visual
---
1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility *(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))*.
3. Download the pipeline and test it on a minimal dataset with a single command:
``` bash
nextflow run nf-core/pathogensurveillance -profile test,YOURPROFILE --outdir <OUTDIR> --download_bakta_db true -resume
```
Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
> - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
> - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
> - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
> - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
4. Start running your own analysis:
<!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
``` bash
nextflow run nf-core/pathogensurveillance --input samplesheet.csv --outdir <OUTDIR> --download_bakta_db true -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> -resume
```
You can also try running a small example dataset hosted with the source code using the following command (no need to download anything):
``` bash
nextflow run nf-core/pathogensurveillance --input https://raw.githubusercontent.com/grunwaldlab/pathogensurveillance/master/test/data/metadata_small.csv --outdir test_out --download_bakta_db true -profile docker -resume
```