Snippet is a programming term for a small region of re-usable source code, machine code, or text, and Nextflow is both a Domain-Specific Language for writing data pipelines and a pipeline orchestrator. For more information about Nextflow, check the official site and documentation. For community training material, this link is a greaaaaaat place to start! 😃
This repository contains a collection of numerous solutions I have worked on throughout the past months as a Nextflow and nf-core Developer Advocate at Seqera Labs providing community support to numerous users around the world. I haven't saved all the snippets I created, but as I have now answered over 500 questions in this period, there are indeed quite a few I have kept when I found the solution interesting enough 😆
Below, you'll find links to Markdown documents in this repository explaining the issue followed by the snippet that solves it.
- Get first N elements from a channel
- Get last N elements from a channel
- Filter items within a list in tuples within your channels
- Filter tuples within your channel
- Flatten multiple-item tuple to 2-item tuple keeping key
- Recreate
countByoperator for channels consisting of single elements or tuples - Set operations with channels
- Filter output channel elements based on file size or file content
- Sort lexicographically paths in a list within a tuple
- Provide multiple paths from a channel as a string to a command
- Guarantee tuple structure in a channel
- Group based on two keys, sort based on another one
- Prepare assets without running the pipeline
- Organize output files according to some pattern, and organize everything else in a different path
- Capture multiple values provided with a pipeline parameter
- Query attributes of objects
- Piping with multiple processes at the same time
- Get the
publishDirpaths for a specific task - Request the maximum number of available CPU cores for a process
- Pass config settings as a command line argument instead of a config file
- Multiple instances of the same file provided to the same task
- Save configuration files used in a specific run
- Compose configurations in the
nextflow.configfile - Run some processes outside containers
- Run containers of specific processes without root access
If you're looking for more snippets, you can find plenty at Nextflow Patterns.