VERSE
ebde9ba68f
- I think it would be better if one for commands only, one for the spec handling core logic so people won't be confused by the core logic inside the commands folder (cleaner I guess) - Regen docs
74 lines
5.0 KiB
Go
74 lines
5.0 KiB
Go
package sys
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import (
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"github.com/versenilvis/iris/spec"
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)
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func init() {
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spec.Register(&spec.Spec{
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Name: "nextflow",
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Description: "Session ID",
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Subcommands: []spec.Subcommand{
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{Name: "clean", Description: "Clean up project cache and work directories (Default: last run)"},
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{Name: "clone", Description: "Clone a project into a folder"},
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{Name: "config", Description: "Print a project configuration"},
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{Name: "console", Description: "Launch Nextflow interactive console"},
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{Name: "drop", Description: "Delete the local copy of a project"},
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{Name: "help", Description: "Print the usage help for a command"},
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{Name: "info", Description: "Print project and system runtime information"},
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{Name: "kuberun", Description: "Execute a workflow in a Kubernetes cluster (experimental)"},
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{Name: "list", Description: "List all downloaded projects"},
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{Name: "log", Description: "Print executions log and runtime info"},
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{Name: "pull", Description: "Download or update a project"},
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{Name: "run", Description: "Execute a pipeline project"},
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{Name: "secrets", Description: "Handle and manage sensitive information for pipeline execution in a safe manner"},
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{Name: "get", Description: "Allows retrieving a secret value e.g. nextflow secrets get FOO"},
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{Name: "delete", Description: "Allows deleting an existing secret e.g. nextflow secrets delete FOO"},
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{Name: "self-update", Description: "Update nextflow runtime to the latest available version"},
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{Name: "view", Description: "View project script file(s)"},
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},
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Options: []spec.Option{
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{Name: "-after", Description: "Clean up runs executed after the specified one"},
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{Name: "-before", Description: "Clean up runs executed before the specified one"},
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{Name: "-but", Description: "Clean up all runs except the specified one"},
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{Name: "-n", Description: "Print names of file to be removed without deleting them (Default: false)"},
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{Name: "-f", Description: "Force clean command (Default: false)"},
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{Name: "-h", Description: "Print the command usage (Default: false)"},
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{Name: "-k", Description: "Do not print names of files removed (Default: false)"},
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{Name: "-hub", Description: "Service hub where the project is hosted (Default: GitHub)"},
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{Name: "-r", Description: "Revision to clone - It can be a git branch, tag or revision number"},
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{Name: "-user", Description: "Private repository user name"},
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{Name: "-flat", Description: "Print config using flat notation (Default: false)"},
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{Name: "-profile", Description: "Choose a configuration profile"},
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{Name: "-properties", Description: "Prints config using Java properties notatio (Default: false)"},
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{Name: "-a", Description: "Show all configuration profiles"},
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{Name: "-sort", Description: "Sort config attributes (Default: false)"},
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{Name: "-u", Description: "Check for remote updates (Default: false)"},
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{Name: "-d", Description: "Show detailed information (Default: false)"},
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{Name: "-o", Description: "Output format, either: text (default), json, yaml"},
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{Name: "-E", Description: "Exports all current system environment (Default: false)"},
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{Name: "-ansi-log", Description: "Enable/disable ANSI console logging"},
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{Name: "-bucket-dir", Description: "Remote bucket where intermediate result files are stored"},
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{Name: "-cache", Description: "Enable/disable processes caching"},
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{Name: "-disable-jobs-cancellation", Description: "Prevent the cancellation of child jobs on execution termination"},
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{Name: "-dsl1", Description: "Execute the workflow using DSL1 syntax (Default: false)"},
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{Name: "-dsl2", Description: "Execute the workflow using DSL2 syntax (Default: false)"},
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{Name: "-dump-channels", Description: "Dump channels for debugging purpose"},
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{Name: "-dump-hashes", Description: "Dump task hash keys for debugging purpose (Default: false)"},
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{Name: "-e", Description: "Entry workflow name to be executed"},
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{Name: "-head-cpus", Description: "Specify number of CPUs requested for the Nextflow pod (Default: 0)"},
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{Name: "-head-memory", Description: "Specify amount of memory requested for the Nextflow pod"},
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{Name: "-latest", Description: "Pull latest changes before run (Default: false)"},
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{Name: "-lib", Description: "Library extension path"},
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{Name: "-main-script", Description: "The script file to be executed when launching a project directory or repository"},
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{Name: "-name", Description: "Assign a mnemonic name to the a pipeline run"},
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{Name: "-offline", Description: "Do not check for remote project updates (Default: false)"},
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{Name: "-params-file", Description: "Load script parameters from a JSON/YAML file"},
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{Name: "-plugins", Description: "Specify the plugins to be applied for this run e.g. nf-amazon,nf-tower"},
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{Name: "-pod-image", Description: "Specify the container image for the Nextflow pod"},
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{Name: "-process", Description: "Set process options. Syntax: -process.key=value (Default: {}"},
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{Name: "-qs", Description: "Max number of processes that can be executed in parallel by each executor"},
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},
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})
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}
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