NGI-NextflowDocs

Depreciation Notice

This project has been archived and is no longer maintained. The information contained is likely to be out of date and might be incorrect in some cases.

We recommend to have a look at Nextflow documentation or at the nf-core website, or to join the gitter channels for some direct contact with developers: nextflow channel or nf-core Lobby.

Common documentation for National Genomics Infrastructure pipelines built with Nextflow. Some variables are specific to Swedish UPPMAX cluster, but can be easily modified to suit any clusters.

Install Nextflow

See the Install documentation

Common options

See the options documentation

Common configuration besides basic required stuff

Configuration Loading

Config variables (eg. params.something) are loaded in the following order:

1. Pipeline script
2. Home directory (~/.nextflow/config)
3. Pipeline script directory (pipeline/nextflow.config)
4. Launch directory (./nextflow.config)
5. Specified config file (-c my_config)
6. Command line (--something)

Anything specified in more than one location will be overwritten by subsequent loads. The command line has preference over everything.

Best practices / snippets

See Example Pipeline

Troubleshooting nextflow

Check the work directory, and especially the last one (which is the one that failed) for information about the failed process, and if needed, you can go up the chain of processes.