otty / apps

All apps/Snakemake

Snakemake

snakemake

Runs as snakemake|Linux|snakemake.github.io

Open form in Otty otty.toml

Sync rules

What travels, what stays, what never leaves

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

· ~/.config/snakemake/ Sync

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

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

id = "snakemake"

name = "Snakemake"

homepage = "https://snakemake.github.io/"

executables = ["snakemake"]

platforms = ["linux"]

[dotfiles]

# The official CLI documentation describes global user profiles under

# $HOME/.config/snakemake (and says the profile directory contains the YAML

# defaults for command-line options). This is the XDG config root on Linux.

# https://snakemake.readthedocs.io/en/latest/executing/cli.html#profiles

paths = ["[configHome]/snakemake/"]

secret = []

[commands]

format = 1

label = "Run a workflow"

description = "Run or preview a Snakefile workflow. Cluster, container, conda, report and plugin options are left out."

quality = "ai-draft"

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

[[commands.source]]

id = "snakemake-man"

kind = "manual"

url = "https://manpages.debian.org/unstable/snakemake/snakemake.1.en.html"

revision = "Debian snakemake(1)"

evidence = '''usage: snakemake [-h] [--snakefile FILE] [--cores [N]] [--configfile FILE] [--directory DIR] [--dryrun] [--printshellcmds] [--keep-going] [--forceall] [--reason] [--unlock] [--rerun-incomplete] [target [target ...]]

--snakefile

FILE, -s FILE

--cores [N],

--jobs [N], -j [N]

Use at most N cores in parallel (default: 1).

--configfile

FILE

--list,

-l

Show available rules in given Snakefile.

--directory

DIR, -d DIR

--dryrun,

-n

Do not execute anything.

--printshellcmds,

-p

--dag

--keep-going,

-k

--forceall,

-F

--reason,

-r

--unlock

Remove a lock on the working directory.

--rerun-incomplete,

--ri'''

[[commands.field]]

id = "targets"

label = "Targets"

description = "Rules or files to build. Empty builds the first rule."

type = "string"

position = 0

multiple = true

sources = ["snakemake-man"]

[[commands.field]]

id = "cores"

label = "Cores"

description = "Maximum cores in parallel."

type = "integer"

option = ["--cores", "-j"]

sources = ["snakemake-man"]

[[commands.field]]

id = "snakefile"

label = "Snakefile"

type = "path"

option = ["--snakefile", "-s"]

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

sources = ["snakemake-man"]

[[commands.field]]

id = "configfile"

label = "Config file"

type = "path"

option = ["--configfile"]

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

sources = ["snakemake-man"]

[[commands.field]]

id = "directory"

label = "Working directory"

type = "path"

option = ["--directory", "-d"]

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

sources = ["snakemake-man"]

[[commands.field]]

id = "dryrun"

label = "Dry run"

type = "boolean"

option = ["--dryrun", "-n"]

sources = ["snakemake-man"]

[[commands.field]]

id = "printshellcmds"

label = "Print shell commands"

type = "boolean"

option = ["--printshellcmds", "-p"]

sources = ["snakemake-man"]

[[commands.field]]

id = "reason"

label = "Print reason for each job"

type = "boolean"

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

sources = ["snakemake-man"]

[[commands.field]]

id = "keep_going"

label = "Keep going after failures"

type = "boolean"

option = ["--keep-going", "-k"]

sources = ["snakemake-man"]

[[commands.field]]

id = "forceall"

label = "Force re-run of all dependencies"

type = "boolean"

option = ["--forceall", "-F"]

effect = "overwrite"

sources = ["snakemake-man"]

[[commands.field]]

id = "rerun_incomplete"

label = "Re-run incomplete jobs"

type = "boolean"

option = ["--rerun-incomplete", "--ri"]

sources = ["snakemake-man"]

[[commands.field]]

id = "unlock"

label = "Remove working directory lock"

type = "boolean"

option = ["--unlock"]

sources = ["snakemake-man"]

[[commands.field]]

id = "list"

label = "List rules"

type = "boolean"

option = ["--list", "-l"]

sources = ["snakemake-man"]

[[commands.field]]

id = "dag"

label = "Print the job DAG (dot)"

type = "boolean"

option = ["--dag"]

sources = ["snakemake-man"]

[[commands.task]]

id = "dry"

label = "Preview the plan"

set = { dryrun = [true], printshellcmds = [true] }

fields = ["targets", "cores", "snakefile", "dryrun", "printshellcmds", "reason"]

required = []

[[commands.task]]

id = "run"

label = "Run the workflow"

set = { cores = [4] }

fields = ["targets", "cores", "snakefile", "keep_going", "rerun_incomplete"]

required = []

[[commands.task]]

id = "unlock"

label = "Unlock directory"

set = { unlock = [true] }

fields = ["snakefile", "unlock"]

required = []

[[commands.group]]

id = "basic"

label = "Basic"

fields = ["targets", "cores", "snakefile", "dryrun", "printshellcmds", "reason"]

[[commands.group]]

id = "advanced"

label = "Advanced"

fields = ["configfile", "directory", "keep_going", "forceall", "rerun_incomplete", "unlock", "list", "dag"]

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/snakemake. Otty ships with this catalog, so the link only has to name the tool — nothing is downloaded.

Every one of these is generated from the same rules as this page.