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All apps/Snakemake

Snakemake

snakemake
Runs as snakemake|Linux|snakemake.github.io
Open form in Otty otty.toml

Command form

ai-draft · 3 tasks · 14 fields

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

Opens the form; the finished command lands at your prompt, unrun
Run in Otty
otty gui snakemake
Run a workflowExample values, fixed in this page — nothing here reaches a terminal
Basic
Targets
string
Cores
integer
Snakefile
file
Dry run
--dryrun
Print shell commands
--printshellcmds
Print reason for each job
--reason
TasksEach one presets the form for one job
Preview the plan
targetscoressnakefiledryrunprintshellcmdsreason
Run the workflow
targetscoressnakefilekeep_goingrerun_incomplete
Unlock directory
snakefileunlock
ParametersOnly these flags are editable in the form
Targets
Rules or files to build. Empty builds the first rule.
string · positional 0 · repeatable
Cores
Maximum cores in parallel.
integer
--cores-j
Snakefile
path
--snakefile-s
Config file
path
--configfile
Working directory
path
--directory-d
Dry run
boolean
--dryrun-n
Print shell commands
boolean
--printshellcmds-p
Print reason for each job
boolean
--reason-r
Keep going after failures
boolean
--keep-going-k
Force re-run of all dependencies
boolean
--forceall-F
Re-run incomplete jobs
boolean
--rerun-incomplete--ri
Remove working directory lock
boolean
--unlock
List rules
boolean
--list-l
Print the job DAG (dot)
boolean
--dag
SourcesEvery flag above is checked against these
snakemake-man
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…
manualDebian snakemake(1)

manpages.debian.org

Before it fills your prompt, Otty checks the installed snakemake against its version. A form that does not match your version is not offered.