All apps/Nextflow

Nextflow

nextflow

Nextflow is a workflow system for creating scalable, portable, and reproducible workflows.

Runs as nextflow|macOS, Linux, Windows|www.nextflow.io

Open form in Otty otty.toml

Command form

ai-draft · 4 tasks · 19 fields

Global options only; use the Run and Pull subcommands.

Opens the form; the finished command lands at your prompt, unrun

Run in Otty

otty gui nextflow

`nextflow run`

Run pipeline

Execute a pipeline project. Docker image arguments, env/process overrides and container runtimes besides Docker are left out.

Run pipelineExample values, fixed in this page — nothing here reaches a terminal

Basic

Pipeline (name, URL or path)*

string

Revision

string

Profile

string

Params file (JSON/YAML)

file

Work directory

directory

TasksEach one presets the form for one job

Run pipeline

pipelinerevisionprofileparams_filework_dir

Resume last run

pipelineprofileparams_file

ParametersOnly these flags are editable in the form

Pipeline (name, URL or path)

string · positional 0

Revision

string

-r-revision

Profile

string

-profile

Params file (JSON/YAML)

path

-params-file

Work directory

path

-w-work-dir

Run name

string

-name

Resume cached run

boolean

-resume

Run with Docker

boolean

-with-docker

HTML report file

path

-with-report

Trace file

path

-with-trace

Timeline file

path

-with-timeline

Stub run

boolean

-stub

Pull latest first

boolean

-latest

Offline

boolean

-offline

Queue size

integer

-qs-queue-size

`nextflow pull`

Pull project

Download or update a project.

Pull projectExample values, fixed in this page — nothing here reaches a terminal

Basic

Project name or URL*

string

Revision

string

TasksEach one presets the form for one job

Pull project

projectrevision

Update all

all

ParametersOnly these flags are editable in the form

Project name or URL

string · positional 0

Revision

string

-r-revision

Update all projects

boolean

-all

Username

string

-user

SourcesEvery flag above is checked against these

fig

completion

fig

completion

fig

completion

Before it fills your prompt, Otty checks the installed nextflow against its version. A form that does not match your version is not offered.