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"]