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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

Sync rules

What travels, what stays, what never leaves

Nextflow in your home directory Every rule on this page, by file

· config Sync

· scm Never synced

Only what the catalog names. A directory that syncs brings everything inside it except what is listed as excluded here.

apps/nextflow/otty.tomlThe file this page is generated from

id = "nextflow"

name = "Nextflow"

homepage = "https://www.nextflow.io"

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

icon = "SimpleIcons:nextflow"

executables = ["nextflow"]

[dotfiles]

# https://docs.seqera.io/nextflow/config — the configuration files are applied

# in this order, lowest priority first: "$NXF_HOME/config (defaults to

# $HOME/.nextflow/config)", then "nextflow.config in the project directory",

# then the launch directory's, then any -c files. Only the first is user-level;

# nextflow.config belongs to the pipeline repository.

paths = ["~/.nextflow/config"]

exclude = []

# https://docs.seqera.io/nextflow/git — "The file $HOME/.nextflow/scm allows you

# to centralize the security credentials required to access private project

# repositories", holding providers.<name>.user, .password and .token. The file

# is that credential store.

secret = ["~/.nextflow/scm"]

# Parsed when a run starts and held for its duration.

# No machine_lines: the user config is executor, container engine and process

# defaults. Cache and work directories are named per run on the command line

# or in the pipeline's own nextflow.config, and the nested Groovy blocks here

# are not something the line-oriented prefix syntax can address safely.

[commands]

format = 1

label = "Nextflow"

description = "Global options only; use the Run and Pull subcommands."

quality = "ai-draft"

base = "fig:nextflow"

parser = { end_of_options = "--", interleave = "permute", long_equals = false, short_attached = false, short_bundles = false }

[[commands.source]]

id = "fig"

kind = "completion"

url = "https://github.com/withfig/autocomplete/blob/master/src/nextflow.ts"

license = "MIT"

[[commands.subcommand]]

path = ["run"]

label = "Run pipeline"

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

[[commands.subcommand.source]]

id = "fig"

kind = "completion"

url = "https://github.com/withfig/autocomplete/blob/master/src/nextflow.ts"

license = "MIT"

[[commands.subcommand.field]]

id = "pipeline"

label = "Pipeline (name, URL or path)"

type = "string"

position = 0

sources = ["fig"]

[[commands.subcommand.field]]

id = "revision"

label = "Revision"

type = "string"

option = ["-r", "-revision"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "profile"

label = "Profile"

type = "string"

option = ["-profile"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "params_file"

label = "Params file (JSON/YAML)"

type = "path"

option = ["-params-file"]

path = { kind = "file", role = "input" }

sources = ["fig"]

[[commands.subcommand.field]]

id = "work_dir"

label = "Work directory"

type = "path"

option = ["-w", "-work-dir"]

path = { kind = "directory", role = "input" }

sources = ["fig"]

[[commands.subcommand.field]]

id = "name"

label = "Run name"

type = "string"

option = ["-name"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "resume"

label = "Resume cached run"

type = "boolean"

option = ["-resume"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "with_docker"

label = "Run with Docker"

type = "boolean"

option = ["-with-docker"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "with_report"

label = "HTML report file"

type = "path"

option = ["-with-report"]

path = { kind = "file", role = "output" }

sources = ["fig"]

[[commands.subcommand.field]]

id = "with_trace"

label = "Trace file"

type = "path"

option = ["-with-trace"]

path = { kind = "file", role = "output" }

sources = ["fig"]

[[commands.subcommand.field]]

id = "with_timeline"

label = "Timeline file"

type = "path"

option = ["-with-timeline"]

path = { kind = "file", role = "output" }

sources = ["fig"]

[[commands.subcommand.field]]

id = "stub"

label = "Stub run"

type = "boolean"

option = ["-stub"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "latest"

label = "Pull latest first"

type = "boolean"

option = ["-latest"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "offline"

label = "Offline"

type = "boolean"

option = ["-offline"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "queue_size"

label = "Queue size"

type = "integer"

option = ["-qs", "-queue-size"]

sources = ["fig"]

[[commands.subcommand.task]]

id = "run"

label = "Run pipeline"

fields = ["pipeline", "revision", "profile", "params_file", "work_dir"]

required = ["pipeline"]

[[commands.subcommand.task]]

id = "resume"

label = "Resume last run"

fields = ["pipeline", "profile", "params_file"]

required = ["pipeline"]

set = { resume = [true] }

[[commands.subcommand.group]]

id = "basic"

label = "Basic"

fields = ["pipeline", "revision", "profile", "params_file", "work_dir", "resume", "with_docker"]

[[commands.subcommand.group]]

id = "advanced"

label = "Advanced"

fields = ["name", "with_report", "with_trace", "with_timeline", "stub", "latest", "offline", "queue_size"]

[[commands.subcommand]]

path = ["pull"]

label = "Pull project"

description = "Download or update a project."

[[commands.subcommand.source]]

id = "fig"

kind = "completion"

url = "https://github.com/withfig/autocomplete/blob/master/src/nextflow.ts"

license = "MIT"

[[commands.subcommand.field]]

id = "project"

label = "Project name or URL"

type = "string"

position = 0

sources = ["fig"]

[[commands.subcommand.field]]

id = "revision"

label = "Revision"

type = "string"

option = ["-r", "-revision"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "all"

label = "Update all projects"

type = "boolean"

option = ["-all"]

sources = ["fig"]

[[commands.subcommand.field]]

id = "user"

label = "Username"

type = "string"

option = ["-user"]

sources = ["fig"]

[[commands.subcommand.task]]

id = "pull"

label = "Pull project"

fields = ["project", "revision"]

required = ["project"]

[[commands.subcommand.task]]

id = "pull-all"

label = "Update all"

fields = ["all"]

required = []

set = { all = [true] }

[[commands.subcommand.group]]

id = "basic"

label = "Basic"

fields = ["project", "revision", "all"]

[[commands.subcommand.group]]

id = "advanced"

label = "Advanced"

fields = ["user"]

Use it with your dotfile manager

Same data, in the shape your tool already reads

Opens Otty and adds this tool to what it syncs

Opens otty://sync/add/nextflow. Otty ships with this catalog, so the link only has to name the tool — nothing is downloaded.

Every one of these keeps the credential file out.