VERSE
2ef3c90819
- I wrote a scripts to copy and generate all commands missing in iris from fig repo: https://github.com/withfig/autocomplete - Add a new script to generate commands docs about which commands currently are inside commands folder 377d4aac663590e504fe39a92eb4dac4cbd333b2 - Add more icons e64d4e70a1db61e62053460a882e093bd6373ab1
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/commands/core"
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)
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func init() {
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core.Register(&core.Spec{
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Name: "nextflow",
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Description: "Session ID",
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Subcommands: []core.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: []core.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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