https://github.com/mribeirodantas/nextflowsnippets
This repository hosts a large collection of Nextflow snippets
https://github.com/mribeirodantas/nextflowsnippets
nextflow nextflow-language pipeline programming snippets workflow
Last synced: 9 months ago
JSON representation
This repository hosts a large collection of Nextflow snippets
- Host: GitHub
- URL: https://github.com/mribeirodantas/nextflowsnippets
- Owner: mribeirodantas
- License: apache-2.0
- Created: 2023-03-26T20:58:03.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2025-01-26T13:50:58.000Z (11 months ago)
- Last Synced: 2025-01-26T14:29:47.556Z (11 months ago)
- Topics: nextflow, nextflow-language, pipeline, programming, snippets, workflow
- Homepage:
- Size: 85.9 KB
- Stars: 57
- Watchers: 4
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 
Nextflow Snippets
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](https://www.nextflow.io) and [documentation](https://www.nextflow.io/docs/latest/). For community training material, [this link](https://training.nextflow.io) is a greaaaaaat place to start! :smiley:
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](https://seqera.io) 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 :satisfied:
## List of snippets by category
Below, you'll find links to Markdown documents in this repository explaining the issue followed by the snippet that solves it.
### Using Channel Operators and Factories
- [Get first N elements from a channel](snippets/get_first_N_from_channel.md)
- [Get last N elements from a channel](snippets/get_last_N_from_channel.md)
- [Filter items within a list in tuples within your channels](snippets/filter_items_within_tuples_within_your_channel.md)
- [Filter tuples within your channel](snippets/filter_tuples_within_your_channel.md)
- [Flatten multiple-item tuple to 2-item tuple keeping key](snippets/flatten_multiple_item_tuples_to_simple_tuple.md)
- [Recreate `countBy` operator for channels consisting of single elements or tuples](snippets/countBy.md)
- [Set operations with channels](snippets/set_operations.md)
- [Filter output channel elements based on file size or file content](snippets/filter_based_on_size_content.md)
- [Sort lexicographically paths in a list within a tuple](snippets/sort_lexicographically_list_in_tuple.md)
- [Provide multiple paths from a channel as a string to a command](snippets/joining_paths_as_string_to_command.md)
- [Guarantee tuple structure in a channel](snippets/guarantee_tuple_structure.md)
- [Group based on two keys, sort based on another one](snippets/grouptuple_sort_metamap.md)
- [Add ending condition to `watchPath`](snippets/end_condition_watchpath.md)
### Misc
- [Prepare assets without running the pipeline](snippets/prepare_assets_wo_running_pipeline.md)
- [Organize output files according to some pattern, and organize everything else in a different path](snippets/organize_publishdir_rest.md)
- [Capture multiple values provided with a pipeline parameter](snippets/capture_multi_values_pipeline_parameter.md)
- [Query attributes of objects](snippets/query_object_attributes.md)
- [Piping with multiple processes at the same time](snippets/pipe_multiple_processes.md)
- [Get the `publishDir` paths for a specific task](snippets/get_task_publishDir.md)
- [Request the maximum number of available CPU cores for a process](snippets/get_max_avail_cpus.md)
- [Pass config settings as a command line argument instead of a config file](snippets/config_cmd_instead_file.md)
- [Multiple instances of the same file provided to the same task](snippets/same_file_multiple_times.md)
- [Save configuration files used in a specific run](snippets/save_configs.md)
- [Compose configurations in the `nextflow.config` file](snippets/composing_nextflow_config.md)
- [Run some processes outside containers](snippets/no_container_per_process.md)
- [Run containers of specific processes without root access](snippets/container_no_root.md)
## Nextflow Patterns
If you're looking for more snippets, you can find plenty at [Nextflow Patterns](https://nextflow-io.github.io/patterns/).