1SNAKEMAKE(1) User Commands SNAKEMAKE(1)
2
6 snakemake - Metapackage for snakemake: azure extras
7
9 usage: snakemake [-h] [--dry-run] [--profile PROFILE]
10 [--workflow-profile WORKFLOW_PROFILE] [--cache [RULE ...]]
12 [--snakefile FILE] [--cores [N]] [--jobs [N]] [--local-cores N]
13 [--resources [NAME=INT ...]] [--set-threads RULE=THREADS
14 [RULE=THREADS ...]] [--max-threads MAX_THREADS] [--set-re‐
15 sources RULE:RESOURCE=VALUE [RULE:RESOURCE=VALUE ...]]
16 [--set-scatter NAME=SCATTERITEMS [NAME=SCATTERITEMS ...]]
17 [--set-resource-scopes RESOURCE=[global|local] [RE‐
18 SOURCE=[global|local] ...]] [--default-resources [NAME=INT
19 ...]] [--preemption-default PREEMPTION_DEFAULT] [--pre‐
20 emptible-rules PREEMPTIBLE_RULES [PREEMPTIBLE_RULES ...]]
21 [--config [KEY=VALUE ...]] [--configfile FILE [FILE ...]]
22 [--envvars VARNAME [VARNAME ...]] [--directory DIR] [--touch]
23 [--keep-going] [--rerun-triggers {mtime,params,input,soft‐
24 ware-env,code} [{mtime,params,input,software-env,code} ...]]
25 [--force] [--forceall] [--forcerun [TARGET ...]] [--prioritize
26 TARGET [TARGET ...]] [--batch RULE=BATCH/BATCHES] [--until TAR‐
27 GET [TARGET ...]] [--omit-from TARGET [TARGET ...]] [--re‐
28 run-incomplete] [--shadow-prefix DIR] [--scheduler
29 [{ilp,greedy}]] [--wms-monitor [WMS_MONITOR]] [--wms-monitor-arg
30 [NAME=VALUE ...]] [--scheduler-ilp-solver {}] [--sched‐
31 uler-solver-path SCHEDULER_SOLVER_PATH] [--conda-base-path
32 CONDA_BASE_PATH] [--no-subworkflows] [--groups GROUPS [GROUPS
33 ...]] [--group-components GROUP_COMPONENTS [GROUP_COMPONENTS
34 ...]] [--report [FILE]] [--report-stylesheet CSSFILE]
35 [--draft-notebook TARGET] [--edit-notebook TARGET] [--note‐
36 book-listen IP:PORT] [--lint [{text,json}]] [--gener‐
37 ate-unit-tests [TESTPATH]] [--containerize] [--export-cwl FILE]
38 [--list] [--list-target-rules] [--dag] [--rulegraph] [--file‐
39 graph] [--d3dag] [--summary] [--detailed-summary] [--archive
40 FILE] [--cleanup-metadata FILE [FILE ...]] [--cleanup-shadow]
41 [--skip-script-cleanup] [--unlock] [--list-version-changes]
42 [--list-code-changes] [--list-input-changes]
43 [--list-params-changes] [--list-untracked] [--delete-all-output]
44 [--delete-temp-output] [--bash-completion] [--keep-incomplete]
45 [--drop-metadata] [--version] [--reason] [--gui [PORT]]
46 [--printshellcmds] [--debug-dag] [--stats FILE] [--nocolor]
47 [--quiet [{progress,rules,all} ...]] [--print-compilation]
48 [--verbose] [--force-use-threads] [--allow-ambiguity] [--nolock]
49 [--ignore-incomplete] [--max-inventory-time SECONDS] [--la‐
50 tency-wait SECONDS] [--wait-for-files [FILE ...]]
51 [--wait-for-files-file FILE] [--notemp] [--all-temp] [--keep-re‐
52 mote] [--keep-target-files] [--allowed-rules ALLOWED_RULES [AL‐
53 LOWED_RULES ...]] [--target-jobs TARGET_JOBS [TARGET_JOBS ...]]
54 [--local-groupid LOCAL_GROUPID] [--max-jobs-per-second
55 MAX_JOBS_PER_SECOND] [--max-status-checks-per-second MAX_STA‐
56 TUS_CHECKS_PER_SECOND] [-T RETRIES] [--attempt ATTEMPT] [--wrap‐
57 per-prefix WRAPPER_PREFIX] [--default-remote-provider
58 {S3,GS,FTP,SFTP,S3Mocked,gfal,gridftp,iRODS,AzBlob,XRootD}]
59 [--default-remote-prefix DEFAULT_REMOTE_PREFIX] [--no-shared-fs]
60 [--greediness GREEDINESS] [--no-hooks] [--overwrite-shellcmd
61 OVERWRITE_SHELLCMD] [--debug] [--runtime-profile FILE] [--mode
62 {0,1,2}] [--show-failed-logs] [--log-handler-script FILE]
63 [--log-service {none,slack,wms}] [--slurm] [--cluster CMD |
64 --cluster-sync CMD | --drmaa [ARGS]] [--cluster-config FILE]
65 [--immediate-submit] [--jobscript SCRIPT] [--jobname NAME]
66 [--cluster-status CLUSTER_STATUS] [--cluster-cancel CLUSTER_CAN‐
67 CEL] [--cluster-cancel-nargs CLUSTER_CANCEL_NARGS] [--clus‐
68 ter-sidecar CLUSTER_SIDECAR] [--drmaa-log-dir DIR] [--kubernetes
69 [NAMESPACE]] [--container-image IMAGE] [--k8s-cpu-scalar FLOAT]
70 [--k8s-service-account-name SERVICEACCOUNTNAME] [--tibanna]
71 [--tibanna-sfn TIBANNA_SFN] [--precommand PRECOMMAND]
72 [--tibanna-config TIBANNA_CONFIG [TIBANNA_CONFIG ...]]
73 [--google-lifesciences] [--google-lifesciences-regions
74 GOOGLE_LIFESCIENCES_REGIONS [GOOGLE_LIFESCIENCES_REGIONS ...]]
75 [--google-lifesciences-location GOOGLE_LIFESCIENCES_LOCATION]
76 [--google-lifesciences-keep-cache] [--google-lifesciences-ser‐
77 vice-account-email GOOGLE_LIFESCIENCES_SERVICE_ACCOUNT_EMAIL]
78 [--google-lifesciences-network GOOGLE_LIFESCIENCES_NETWORK]
79 [--google-lifesciences-subnetwork GOOGLE_LIFESCIENCES_SUBNET‐
80 WORK] [--az-batch] [--az-batch-enable-autoscale] [--az-batch-ac‐
81 count-url [AZ_BATCH_ACCOUNT_URL]] [--flux] [--tes URL]
82 [--use-conda] [--conda-not-block-search-path-envvars]
83 [--list-conda-envs] [--conda-prefix DIR] [--conda-cleanup-envs]
84 [--conda-cleanup-pkgs [{tarballs,cache}]] [--conda-cre‐
85 ate-envs-only] [--conda-frontend {conda,mamba}] [--use-singular‐
86 ity] [--singularity-prefix DIR] [--singularity-args ARGS]
87 [--cleanup-containers] [--use-envmodules] [target ...]
88 Snakemake is a Python based language and execution environment for GNU
90 Makelike workflows.
91 options:
93 -h, --help
94 show this help message and exit
95 EXECUTION:
97 target Targets to build. May be rules or files. (default: None)
98 --dry-run, --dryrun, -n
100 Do not execute anything, and display what would be done. If you
101 have a very large workflow, use --dry-run --quiet to just print
102 a summary of the DAG of jobs. (default: False)
103 --profile PROFILE
105 Name of profile to use for configuring Snakemake. Snakemake
106 will search for a corresponding folder in /etc/xdg/snakemake and
107 /builddir/.config/snakemake. Alternatively, this can be an ab‐
108 solute or relative path. The profile folder has to contain a
109 file 'config.yaml'. This file can be used to set default values
110 for command line options in YAML format. For example, '--cluster
111 qsub' becomes 'cluster: qsub' in the YAML file. Profiles can be
112 obtained from https://github.com/snakemake-profiles. The profile
113 can also be set via the environment variable $SNAKEMAKE_PROFILE.
114 To override this variable and use no profile at all, provide the
115 value 'none' to this argument. [env var: SNAKEMAKE_PROFILE] (de‐
116 fault: None)
117 --workflow-profile WORKFLOW_PROFILE
119 Path (relative to current directory) to workflow specific pro‐
120 file folder to use for configuring Snakemake with parameters
121 specific for this workflow (like resources). If this flag is not
122 used, Snakemake will by default use 'profiles/default' if
123 present (searched both relative to current directory and rela‐
124 tive to Snakefile, in this order). For skipping any workflow
125 specific profile provide the special value 'none'. Settings made
126 in the workflow profile will override settings made in the gen‐
127 eral profile (see --profile). The profile folder has to contain
128 a file 'config.yaml'. This file can be used to set default val‐
129 ues for command line options in YAML format. For example,
130 '--cluster qsub' becomes 'cluster: qsub' in the YAML file. It is
131 advisable to use the workflow profile to set or overwrite e.g.
132 workflow specific resources like the amount of threads of a par‐
133 ticular rule or the amount of memory needed. Note that in such
134 cases, the arguments may be given as nested YAML mappings in the
135 profile, e.g. 'setthreads: myrule: 4' instead of 'set-threads:
136 myrule=4'. (default: None)
137 --cache [RULE ...]
139 Store output files of given rules in a central cache given by
140 the environment variable $SNAKEMAKE_OUTPUT_CACHE. Likewise, re‐
141 trieve output files of the given rules from this cache if they
142 have been created before (by anybody writing to the same cache),
143 instead of actually executing the rules. Output files are iden‐
144 tified by hashing all steps, parameters and software stack
145 (conda envs or containers) needed to create them. (default:
146 None)
147 --snakefile FILE, -s FILE
149 The workflow definition in form of a snakefile. Usually, you
150 should not need to specify this. By default, Snakemake will
151 search for 'Snakefile', 'snakefile', 'workflow/Snakefile',
152 'workflow/snakefile' beneath the current working directory, in
153 this order. Only if you definitely want a different layout, you
154 need to use this parameter. (default: None)
155 --cores [N], -c [N]
157 Use at most N CPU cores/jobs in parallel. If N is omitted or
158 'all', the limit is set to the number of available CPU cores. In
159 case of cluster/cloud execution, this argument sets the maximum
160 number of cores requested from the cluster or cloud scheduler.
161 (See https://snakemake.readthedocs.io/en/stable/snakef
162 iles/rules.html#resources-remote-execution for more info)This
163 number is available to rules via workflow.cores. (default: None)
164 --jobs [N], -j [N]
166 Use at most N CPU cluster/cloud jobs in parallel. For local exe‐
167 cution this is an alias for --cores. Note: Set to 'unlimited' in
168 case, this does not play a role. (default: None)
169 --local-cores N
171 In cluster/cloud mode, use at most N cores of the host machine
172 in parallel (default: number of CPU cores of the host). The
173 cores are used to execute local rules. This option is ignored
174 when not in cluster/cloud mode. (default: 6)
175 --resources [NAME=INT ...], --res [NAME=INT ...]
177 Define additional resources that shall constrain the scheduling
178 analogously to --cores (see above). A resource is defined as a
179 name and an integer value. E.g. --resources mem_mb=1000. Rules
180 can use resources by defining the resource keyword, e.g. re‐
181 sources: mem_mb=600. If now two rules require 600 of the re‐
182 source 'mem_mb' they won't be run in parallel by the scheduler.
183 In cluster/cloud mode, this argument will also constrain the
184 amount of resources requested from the server. (See
185 https://snakemake.readthedocs.io/en/s table/snake‐
186 files/rules.html#resources-remote-execution for more info) (de‐
187 fault: None)
188 --set-threads RULE=THREADS [RULE=THREADS ...]
190 Overwrite thread usage of rules. This allows to finetune work‐
191 flow parallelization. In particular, this is helpful to target
192 certain cluster nodes by e.g. shifting a rule to use more, or
193 less threads than defined in the workflow. Thereby, THREADS has
194 to be a positive integer, and RULE has to be the name of the
195 rule. (default: None)
196 --max-threads MAX_THREADS
198 Define a global maximum number of threads available to any rule.
199 Rules requesting more threads (via the threads keyword) will
200 have their values reduced to the maximum. This can be useful
201 when you want to restrict the maximum number of threads without
202 modifying the workflow definition or overwriting rules individu‐
203 ally with --set-threads. (default: None)
204 --set-resources RULE:RESOURCE=VALUE [RULE:RESOURCE=VALUE ...]
206 Overwrite resource usage of rules. This allows to fine-tune
207 workflow resources. In particular, this is helpful to target
208 certain cluster nodes by e.g. defining a certain partition for
209 a rule, or overriding a temporary directory. Thereby, VALUE has
210 to be a positive integer or a string, RULE has to be the name of
211 the rule, and RESOURCE has to be the name of the resource. (de‐
212 fault: None)
213 --set-scatter NAME=SCATTERITEMS [NAME=SCATTERITEMS ...]
215 Overwrite number of scatter items of scattergather processes.
216 This allows to fine-tune workflow parallelization. Thereby,
217 SCATTERITEMS has to be a positive integer, and NAME has to be
218 the name of the scattergather process defined via a scatter‐
219 gather directive in the workflow. (default: None)
220 --set-resource-scopes RESOURCE=[global|local] [RESOURCE=[global|local]
222 ...]
223 Overwrite resource scopes. A scope determines how a constraint
224 is reckoned in cluster execution. With RESOURCE=local, a con‐
225 straint applied to RESOURCE using --resources will be considered
226 the limit for each group submission. With RESOURCE=global, the
227 constraint will apply across all groups cumulatively. By de‐
228 fault, only `mem_mb` and `disk_mb` are considered local, all
229 other resources are global. This may be modified in the snake‐
230 file using the `resource_scopes:` directive. Note that number
231 of threads, specified via --cores, is always considered local.
232 (See https://snakemake.readth edocs.io/en/stable/snake‐
233 files/rules.html#resourcesremote-execution for more info) (de‐
234 fault: None)
235 --default-resources [NAME=INT ...], --default-res [NAME=INT ...]
237 Define default values of resources for rules that do not define
238 their own values. In addition to plain integers, python expres‐
239 sions over inputsize are allowed (e.g. '2*input.size_mb'). The
240 inputsize is the sum of the sizes of all input files of a rule.
241 By default, Snakemake assumes a default for mem_mb, disk_mb, and
242 tmpdir (see below). This option allows to add further defaults
243 (e.g. account and partition for slurm) or to overwrite these de‐
244 fault values. The defaults are 'mem_mb=max(2*input.size_mb,
245 1000)', 'disk_mb=max(2*input.size_mb, 1000)' (i.e., default disk
246 and mem usage is twice the input file size but at least 1GB),
247 and the system temporary directory (as given by $TMPDIR, $TEMP,
248 or $TMP) is used for the tmpdir resource. The tmpdir resource is
249 automatically used by shell commands, scripts and wrappers to
250 store temporary data (as it is mirrored into $TMPDIR, $TEMP, and
251 $TMP for the executed subprocesses). If this argument is not
252 specified at all, Snakemake just uses the tmpdir resource as
253 outlined above. (default: None)
254 --preemption-default PREEMPTION_DEFAULT
256 A preemptible instance can be requested when using the Google
257 Life Sciences API. If you set a --preemptiondefault, all rules
258 will be subject to the default. Specifically, this integer is
259 the number of restart attempts that will be made given that the
260 instance is killed unexpectedly. Note that preemptible instances
261 have a maximum running time of 24 hours. If you want to set pre‐
262 emptible instances for only a subset of rules, use --pre‐
263 emptible-rules instead. (default: None)
264 --preemptible-rules PREEMPTIBLE_RULES [PREEMPTIBLE_RULES ...]
266 A preemptible instance can be requested when using the Google
267 Life Sciences API. If you want to use these instances for a sub‐
268 set of your rules, you can use --preemptible-rules and then
269 specify a list of rule and integer pairs, where each integer in‐
270 dicates the number of restarts to use for the rule's instance in
271 the case that the instance is terminated unexpectedly. --pre‐
272 emptible-rules can be used in combination with --preemption-de‐
273 fault, and will take priority. Note that preemptible instances
274 have a maximum running time of 24. If you want to apply a con‐
275 sistent number of retries across all your rules, use --preemp‐
276 tiondefault instead. Example: snakemake --preemptiondefault 10
277 --preemptible-rules map_reads=3 call_variants=0 (default: None)
278 --config [KEY=VALUE ...], -C [KEY=VALUE ...]
280 Set or overwrite values in the workflow config object. The
281 workflow config object is accessible as variable config inside
282 the workflow. Default values can be set by providing a JSON file
283 (see Documentation). (default: None)
284 --configfile FILE [FILE ...], --configfiles FILE [FILE ...]
286 Specify or overwrite the config file of the workflow (see the
287 docs). Values specified in JSON or YAML format are available in
288 the global config dictionary inside the workflow. Multiple files
289 overwrite each other in the given order. Thereby missing keys in
290 previous config files are extended by following configfiles.
291 Note that this order also includes a config file defined in the
292 workflow definition itself (which will come first). (default:
293 None)
294 --envvars VARNAME [VARNAME ...]
296 Environment variables to pass to cloud jobs. (default: None)
297 --directory DIR, -d DIR
299 Specify working directory (relative paths in the snakefile will
300 use this as their origin). (default: None)
301 --touch, -t
303 Touch output files (mark them up to date without really changing
304 them) instead of running their commands. This is used to pretend
305 that the rules were executed, in order to fool future invoca‐
306 tions of snakemake. Fails if a file does not yet exist. Note
307 that this will only touch files that would otherwise be recre‐
308 ated by Snakemake (e.g. because their input files are newer).
309 For enforcing a touch, combine this with --force, --forceall, or
310 --forcerun. Note however that you lose the provenance informa‐
311 tion when the files have been created in reality. Hence, this
312 should be used only as a last resort. (default: False)
313 --keep-going, -k
315 Go on with independent jobs if a job fails. (default: False)
316 --rerun-triggers {mtime,params,input,software-env,code}
318 [{mtime,params,input,software-env,code} ...]
319 Define what triggers the rerunning of a job. By default, all
320 triggers are used, which guarantees that results are consistent
321 with the workflow code and configuration. If you rather prefer
322 the traditional way of just considering file modification dates,
323 use ' --rerun-trigger mtime'. (default: ['mtime', 'params', 'in‐
324 put', 'software-env', 'code'])
325 --force, -f
327 Force the execution of the selected target or the first rule re‐
328 gardless of already created output. (default: False)
329 --forceall, -F
331 Force the execution of the selected (or the first) rule and all
332 rules it is dependent on regardless of already created output.
333 (default: False)
334 --forcerun [TARGET ...], -R [TARGET ...]
336 Force the re-execution or creation of the given rules or files.
337 Use this option if you changed a rule and want to have all its
338 output in your workflow updated. (default: None)
339 --prioritize TARGET [TARGET ...], -P TARGET [TARGET ...]
341 Tell the scheduler to assign creation of given targets (and all
342 their dependencies) highest priority. (EXPERIMENTAL) (default:
343 None)
344 --batch RULE=BATCH/BATCHES
346 Only create the given BATCH of the input files of the given
347 RULE. This can be used to iteratively run parts of very large
348 workflows. Only the execution plan of the relevant part of the
349 workflow has to be calculated, thereby speeding up DAG computa‐
350 tion. It is recommended to provide the most suitable rule for
351 batching when documenting a workflow. It should be some aggre‐
352 gating rule that would be executed only once, and has a large
353 number of input files. For example, it can be a rule that aggre‐
354 gates over samples. (default: None)
355 --until TARGET [TARGET ...], -U TARGET [TARGET ...]
357 Runs the pipeline until it reaches the specified rules or files.
358 Only runs jobs that are dependencies of the specified rule or
359 files, does not run sibling DAGs. (default: None)
360 --omit-from TARGET [TARGET ...], -O TARGET [TARGET ...]
362 Prevent the execution or creation of the given rules or files as
363 well as any rules or files that are downstream of these targets
364 in the DAG. Also runs jobs in sibling DAGs that are independent
365 of the rules or files specified here. (default: None)
366 --rerun-incomplete, --ri
368 Re-run all jobs the output of which is recognized as incomplete.
369 (default: False)
370 --shadow-prefix DIR
372 Specify a directory in which the 'shadow' directory is created.
373 If not supplied, the value is set to the '.snakemake' directory
374 relative to the working directory. (default: None)
375 --scheduler [{ilp,greedy}]
377 Specifies if jobs are selected by a greedy algorithm or by solv‐
378 ing an ilp. The ilp scheduler aims to reduce runtime and hdd us‐
379 age by best possible use of resources. (default: greedy)
380 --wms-monitor [WMS_MONITOR]
382 IP and port of workflow management system to monitor the execu‐
383 tion of snakemake (e.g. http://127.0.0.1:5000) Note that if
384 your service requires an authorization token, you must export
385 WMS_MONITOR_TOKEN in the environment. (default: None)
386 --wms-monitor-arg [NAME=VALUE ...]
388 If the workflow management service accepts extra arguments, pro‐
389 vide. them in key value pairs with --wms-monitor-arg. For exam‐
390 ple, to run an existing workflow using a wms monitor, you can
391 provide the pair id=12345 and the arguments will be provided to
392 the endpoint to first interact with the workflow (default: None)
393 --scheduler-ilp-solver {}
395 Specifies solver to be utilized when selecting ilpscheduler.
396 (default: COIN_CMD)
397 --scheduler-solver-path SCHEDULER_SOLVER_PATH
399 Set the PATH to search for scheduler solver binaries (internal
400 use only). (default: None)
401 --conda-base-path CONDA_BASE_PATH
403 Path of conda base installation (home of conda, mamba, activate)
404 (internal use only). (default: None)
405 --no-subworkflows, --nosw
407 Do not evaluate or execute subworkflows. (default: False)
408 GROUPING:
410 --groups GROUPS [GROUPS ...]
411 Assign rules to groups (this overwrites any group definitions
412 from the workflow). (default: None)
413 --group-components GROUP_COMPONENTS [GROUP_COMPONENTS ...]
415 Set the number of connected components a group is allowed to
416 span. By default, this is 1, but this flag allows to extend
417 this. This can be used to run e.g. 3 jobs of the same rule in
418 the same group, although they are not connected. It can be help‐
419 ful for putting together many small jobs or benefitting of
420 shared memory setups. (default: None)
421 REPORTS:
423 --report [FILE]
424 Create an HTML report with results and statistics. This can be
425 either a .html file or a .zip file. In the former case, all re‐
426 sults are embedded into the .html (this only works for small
427 data). In the latter case, results are stored along with a file
428 report.html in the zip archive. If no filename is given, an em‐
429 bedded report.html is the default. (default: None)
430 --report-stylesheet CSSFILE
432 Custom stylesheet to use for report. In particular, this can be
433 used for branding the report with e.g. a custom logo, see docs.
434 (default: None)
435 NOTEBOOKS:
437 --draft-notebook TARGET
438 Draft a skeleton notebook for the rule used to generate the
439 given target file. This notebook can then be opened in a jupyter
440 server, executed and implemented until ready. After saving, it
441 will automatically be reused in non-interactive mode by Snake‐
442 make for subsequent jobs. (default: None)
443 --edit-notebook TARGET
445 Interactively edit the notebook associated with the rule used to
446 generate the given target file. This will start a local jupyter
447 notebook server. Any changes to the notebook should be saved,
448 and the server has to be stopped by closing the notebook and
449 hitting the 'Quit' button on the jupyter dashboard. Afterwards,
450 the updated notebook will be automatically stored in the path
451 defined in the rule. If the notebook is not yet present, this
452 will create an empty draft. (default: None)
453 --notebook-listen IP:PORT
455 The IP address and PORT the notebook server used for editing the
456 notebook (--edit-notebook) will listen on. (default: local‐
457 host:8888)
458 UTILITIES:
460 --lint [{text,json}]
461 Perform linting on the given workflow. This will print snakemake
462 specific suggestions to improve code quality (work in progress,
463 more lints to be added in the future). If no argument is pro‐
464 vided, plain text output is used. (default: None)
465 --generate-unit-tests [TESTPATH]
467 Automatically generate unit tests for each workflow rule. This
468 assumes that all input files of each job are already present.
469 Rules without a job with present input files will be skipped (a
470 warning will be issued). For each rule, one test case will be
471 created in the specified test folder (.tests/unit by default).
472 After successful execution, tests can be run with 'pytest TEST‐
473 PATH'. (default: None)
474 --containerize
476 Print a Dockerfile that provides an execution environment for
477 the workflow, including all conda environments. (default: False)
478 --export-cwl FILE
480 Compile workflow to CWL and store it in given FILE. (default:
481 None)
482 --list, -l
484 Show available rules in given Snakefile. (default: False)
485 --list-target-rules, --lt
487 Show available target rules in given Snakefile. (default:
488 False)
489 --dag Do not execute anything and print the directed acyclic graph of
491 jobs in the dot language. Recommended use on Unix systems:
492 snakemake --dag | dot | display. Note print statements in your
493 Snakefile may interfere with visualization. (default: False)
494 --rulegraph
496 Do not execute anything and print the dependency graph of rules
497 in the dot language. This will be less crowded than above DAG of
498 jobs, but also show less information. Note that each rule is
499 displayed once, hence the displayed graph will be cyclic if a
500 rule appears in several steps of the workflow. Use this if above
501 option leads to a DAG that is too large. Recommended use on
502 Unix systems: snakemake --rulegraph | dot | display. Note print
503 statements in your Snakefile may interfere with visualization.
504 (default: False)
505 --filegraph
507 Do not execute anything and print the dependency graph of rules
508 with their input and output files in the dot language. This is
509 an intermediate solution between above DAG of jobs and the rule
510 graph. Note that each rule is displayed once, hence the dis‐
511 played graph will be cyclic if a rule appears in several steps
512 of the workflow. Use this if above option leads to a DAG that is
513 too large. Recommended use on Unix systems: snakemake --file‐
514 graph | dot | display. Note print statements in your Snakefile
515 may interfere with visualization. (default: False)
516 --d3dag
518 Print the DAG in D3.js compatible JSON format. (default: False)
519 --summary, -S
521 Print a summary of all files created by the workflow. The has
522 the following columns: filename, modification time, rule ver‐
523 sion, status, plan. Thereby rule version contains the versionthe
524 file was created with (see the version keyword of rules), and
525 status denotes whether the file is missing, its input files are
526 newer or if version or implementation of the rule changed since
527 file creation. Finally the last column denotes whether the file
528 will be updated or created during the next workflow execution.
529 (default: False)
530 --detailed-summary, -D
532 Print a summary of all files created by the workflow. The has
533 the following columns: filename, modification time, rule ver‐
534 sion, input file(s), shell command, status, plan. Thereby rule
535 version contains the version the file was created with (see the
536 version keyword of rules), and status denotes whether the file
537 is missing, its input files are newer or if version or implemen‐
538 tation of the rule changed since file creation. The input file
539 and shell command columns are self explanatory. Finally the last
540 column denotes whether the file will be updated or created dur‐
541 ing the next workflow execution. (default: False)
542 --archive FILE
544 Archive the workflow into the given tar archive FILE. The ar‐
545 chive will be created such that the workflow can be re-executed
546 on a vanilla system. The function needs conda and git to be in‐
547 stalled. It will archive every file that is under git version
548 control. Note that it is best practice to have the Snakefile,
549 config files, and scripts under version control. Hence, they
550 will be included in the archive. Further, it will add input
551 files that are not generated by by the workflow itself and conda
552 environments. Note that symlinks are dereferenced. Supported
553 formats are .tar, .tar.gz, .tar.bz2 and .tar.xz. (default: None)
554 --cleanup-metadata FILE [FILE ...], --cm FILE [FILE ...]
556 Cleanup the metadata of given files. That means that snakemake
557 removes any tracked version info, and any marks that files are
558 incomplete. (default: None)
559 --cleanup-shadow
561 Cleanup old shadow directories which have not been deleted due
562 to failures or power loss. (default: False)
563 --skip-script-cleanup
565 Don't delete wrapper scripts used for execution (default: False)
566 --unlock
568 Remove a lock on the working directory. (default: False)
569 --list-version-changes, --lv
571 List all output files that have been created with a different
572 version (as determined by the version keyword). (default: False)
573 --list-code-changes, --lc
575 List all output files for which the rule body (run or shell)
576 have changed in the Snakefile. (default: False)
577 --list-input-changes, --li
579 List all output files for which the defined input files have
580 changed in the Snakefile (e.g. new input files were added in the
581 rule definition or files were renamed). For listing input file
582 modification in the filesystem, use --summary. (default: False)
583 --list-params-changes, --lp
585 List all output files for which the defined params have changed
586 in the Snakefile. (default: False)
587 --list-untracked, --lu
589 List all files in the working directory that are not used in the
590 workflow. This can be used e.g. for identifying leftover files.
591 Hidden files and directories are ignored. (default: False)
592 --delete-all-output
594 Remove all files generated by the workflow. Use together with
595 --dry-run to list files without actually deleting anything. Note
596 that this will not recurse into subworkflows. Write-protected
597 files are not removed. Nevertheless, use with care! (default:
598 False)
599 --delete-temp-output
601 Remove all temporary files generated by the workflow. Use to‐
602 gether with --dry-run to list files without actually deleting
603 anything. Note that this will not recurse into subworkflows.
604 (default: False)
605 --bash-completion
607 Output code to register bash completion for snakemake. Put the
608 following in your .bashrc (including the accents): `snakemake
609 --bash-completion` or issue it in an open terminal session. (de‐
610 fault: False)
611 --keep-incomplete
613 Do not remove incomplete output files by failed jobs. (default:
614 False)
615 --drop-metadata
617 Drop metadata file tracking information after job finishes.
618 Provenance-information based reports (e.g. --report and the
619 --list_x_changes functions) will be empty or incomplete. (de‐
620 fault: False)
621 --version, -v
623 show program's version number and exit
624 OUTPUT:
626 --reason, -r
627 Print the reason for each executed rule (deprecated, always true
628 now). (default: False)
629 --gui [PORT]
631 Serve an HTML based user interface to the given network and port
632 e.g. 168.129.10.15:8000. By default Snakemake is only available
633 in the local network (default port: 8000). To make Snakemake
634 listen to all ip addresses add the special host address 0.0.0.0
635 to the url (0.0.0.0:8000). This is important if Snakemake is
636 used in a virtualised environment like Docker. If possible, a
637 browser window is opened. (default: None)
638 --printshellcmds, -p
640 Print out the shell commands that will be executed. (default:
641 False)
642 --debug-dag
644 Print candidate and selected jobs (including their wildcards)
645 while inferring DAG. This can help to debug unexpected DAG
646 topology or errors. (default: False)
647 --stats FILE
649 Write stats about Snakefile execution in JSON format to the
650 given file. (default: None)
651 --nocolor
653 Do not use a colored output. (default: False)
654 --quiet [{progress,rules,all} ...], -q [{progress,rules,all} ...]
656 Do not output certain information. If used without arguments, do
657 not output any progress or rule information. Defining 'all' re‐
658 sults in no information being printed at all. (default: None)
659 --print-compilation
661 Print the python representation of the workflow. (default:
662 False)
663 --verbose
665 Print debugging output. (default: False)
666 BEHAVIOR:
668 --force-use-threads
669 Force threads rather than processes. Helpful if shared memory
670 (/dev/shm) is full or unavailable. (default: False)
671 --allow-ambiguity, -a
673 Don't check for ambiguous rules and simply use the first if sev‐
674 eral can produce the same file. This allows the user to priori‐
675 tize rules by their order in the snakefile. (default: False)
676 --nolock
678 Do not lock the working directory (default: False)
679 --ignore-incomplete, --ii
681 Do not check for incomplete output files. (default: False)
682 --max-inventory-time SECONDS
684 Spend at most SECONDS seconds to create a file inventory for the
685 working directory. The inventory vastly speeds up file modifica‐
686 tion and existence checks when computing which jobs need to be
687 executed. However, creating the inventory itself can be slow,
688 e.g. on network file systems. Hence, we do not spend more than a
689 given amount of time and fall back to individual checks for the
690 rest. (default: 20)
691 --latency-wait SECONDS, --output-wait SECONDS, -w SECONDS
693 Wait given seconds if an output file of a job is not present af‐
694 ter the job finished. This helps if your filesystem suffers from
695 latency (default 5). (default: 5)
696 --wait-for-files [FILE ...]
698 Wait --latency-wait seconds for these files to be present before
699 executing the workflow. This option is used internally to handle
700 filesystem latency in cluster environments. (default: None)
701 --wait-for-files-file FILE
703 Same behaviour as --wait-for-files, but file list is stored in
704 file instead of being passed on the commandline. This is useful
705 when the list of files is too long to be passed on the command‐
706 line. (default: None)
707 --notemp, --nt
709 Ignore temp() declarations. This is useful when running only a
710 part of the workflow, since temp() would lead to deletion of
711 probably needed files by other parts of the workflow. (default:
712 False)
713 --all-temp
715 Mark all output files as temp files. This can be useful for CI
716 testing, in order to save space. (default: False)
717 --keep-remote
719 Keep local copies of remote input files. (default: False)
720 --keep-target-files
722 Do not adjust the paths of given target files relative to the
723 working directory. (default: False)
724 --allowed-rules ALLOWED_RULES [ALLOWED_RULES ...]
726 Only consider given rules. If omitted, all rules in Snakefile
727 are used. Note that this is intended primarily for internal use
728 and may lead to unexpected results otherwise. (default: None)
729 --target-jobs TARGET_JOBS [TARGET_JOBS ...]
731 Target particular jobs by RULE:WILDCARD1=VALUE,WILD‐
732 CARD2=VALUE,... This is meant for internal use by Snakemake it‐
733 self only. (default: None)
734 --local-groupid LOCAL_GROUPID
736 Name for local groupid, meant for internal use only. (default:
737 local)
738 --max-jobs-per-second MAX_JOBS_PER_SECOND
740 Maximal number of cluster/drmaa jobs per second, default is 10,
741 fractions allowed. (default: 10)
742 --max-status-checks-per-second MAX_STATUS_CHECKS_PER_SECOND
744 Maximal number of job status checks per second, default is 10,
745 fractions allowed. (default: 10)
746 -T RETRIES, --retries RETRIES, --restart-times RETRIES
748 Number of times to restart failing jobs (defaults to 0). (de‐
749 fault: 0)
750 --attempt ATTEMPT
752 Internal use only: define the initial value of the attempt pa‐
753 rameter (default: 1). (default: 1)
754 --wrapper-prefix WRAPPER_PREFIX
756 Prefix for URL created from wrapper directive (default:
757 https://github.com/snakemake/snakemakewrappers/raw/). Set this
758 to a different URL to use your fork or a local clone of the
759 repository, e.g., use a git URL like
760 'git+file://path/to/your/local/clone@'. (default:
761 https://github.com/snakemake/snakemake-wrappers/raw/)
762 --default-remote-provider
764 {S3,GS,FTP,SFTP,S3Mocked,gfal,gridftp,iRODS,AzBlob,XRootD}
765 Specify default remote provider to be used for all input and
766 output files that don't yet specify one. (default: None)
767 --default-remote-prefix DEFAULT_REMOTE_PREFIX
769 Specify prefix for default remote provider. E.g. a bucket name.
770 (default: )
771 --no-shared-fs
773 Do not assume that jobs share a common file system. When this
774 flag is activated, Snakemake will assume that the filesystem on
775 a cluster node is not shared with other nodes. For example, this
776 will lead to downloading remote files on each cluster node sepa‐
777 rately. Further, it won't take special measures to deal with
778 filesystem latency issues. This option will in most cases only
779 make sense in combination with --default-remote-provider. Fur‐
780 ther, when using --cluster you will have to also provide --clus‐
781 terstatus. Only activate this if you know what you are doing.
782 (default: False)
783 --greediness GREEDINESS
785 Set the greediness of scheduling. This value between 0 and 1 de‐
786 termines how careful jobs are selected for execution. The de‐
787 fault value (1.0) provides the best speed and still acceptable
788 scheduling quality. (default: None)
789 --no-hooks
791 Do not invoke onstart, onsuccess or onerror hooks after execu‐
792 tion. (default: False)
793 --overwrite-shellcmd OVERWRITE_SHELLCMD
795 Provide a shell command that shall be executed instead of those
796 given in the workflow. This is for debugging purposes only. (de‐
797 fault: None)
798 --debug
800 Allow to debug rules with e.g. PDB. This flag allows to set
801 breakpoints in run blocks. (default: False)
802 --runtime-profile FILE
804 Profile Snakemake and write the output to FILE. This requires
805 yappi to be installed. (default: None)
806 --mode {0,1,2}
808 Set execution mode of Snakemake (internal use only). (default:
809 0)
810 --show-failed-logs
812 Automatically display logs of failed jobs. (default: False)
813 --log-handler-script FILE
815 Provide a custom script containing a function 'def log_han‐
816 dler(msg):'. Snakemake will call this function for every logging
817 output (given as a dictionary msg) allowing to e.g. send notifi‐
818 cations in the form of e.g. slack messages or emails. (default:
819 None)
820 --log-service {none,slack,wms}
822 Set a specific messaging service for logging output. Snakemake
823 will notify the service on errors and completed execution. Cur‐
824 rently slack and workflow management system (wms) are supported.
825 (default: None)
826 SLURM:
828 --slurm
829 Execute snakemake rules as SLURM batch jobs according to their
830 'resources' definition. SLURM resources as 'partition',
831 'ntasks', 'cpus', etc. need to be defined per rule within the
832 'resources' definition. Note, that memory can only be defined as
833 'mem_mb' or 'mem_mb_per_cpu' as analogous to the SLURM 'mem' and
834 'mem-per-cpu' flags to sbatch, respectively. Here, the unit is
835 always 'MiB'. In addition '-- default_resources' should contain
836 the SLURM account. (default: False)
837 CLUSTER:
839 --cluster CMD
840 Execute snakemake rules with the given submit command, e.g.
841 qsub. Snakemake compiles jobs into scripts that are submitted to
842 the cluster with the given command, once all input files for a
843 particular job are present. The submit command can be decorated
844 to make it aware of certain job properties (name, rulename, in‐
845 put, output, params, wildcards, log, threads and dependencies
846 (see the argument below)), e.g.: $ snakemake --cluster 'qsub -pe
847 threaded {threads}'. (default: None)
848 --cluster-sync CMD
850 cluster submission command will block, returning the remote exit
851 status upon remote termination (for example, this should be used
852 if the cluster command is 'qsub -sync y' (SGE) (default: None)
853 --drmaa [ARGS]
855 Execute snakemake on a cluster accessed via DRMAA, Snakemake
856 compiles jobs into scripts that are submitted to the cluster
857 with the given command, once all input files for a particular
858 job are present. ARGS can be used to specify options of the un‐
859 derlying cluster system, thereby using the job properties name,
860 rulename, input, output, params, wildcards, log, threads and de‐
861 pendencies, e.g.: --drmaa ' -pe threaded {threads}'. Note that
862 ARGS must be given in quotes and with a leading whitespace. (de‐
863 fault: None)
864 --cluster-config FILE, -u FILE
866 A JSON or YAML file that defines the wildcards used in 'cluster'
867 for specific rules, instead of having them specified in the
868 Snakefile. For example, for rule 'job' you may define: { 'job' :
869 { 'time' : '24:00:00' } } to specify the time for rule 'job'.
870 You can specify more than one file. The configuration files are
871 merged with later values overriding earlier ones. This option
872 is deprecated in favor of using --profile, see docs. (default:
873 [])
874 --immediate-submit, --is
876 Immediately submit all jobs to the cluster instead of waiting
877 for present input files. This will fail, unless you make the
878 cluster aware of job dependencies, e.g. via: $ snakemake --clus‐
879 ter 'sbatch --dependency {dependencies}. Assuming that your sub‐
880 mit script (here sbatch) outputs the generated job id to the
881 first stdout line, {dependencies} will be filled with space sep‐
882 arated job ids this job depends on. Does not work for workflows
883 that contain checkpoint rules. (default: False)
884 --jobscript SCRIPT, --js SCRIPT
886 Provide a custom job script for submission to the cluster. The
887 default script resides as 'jobscript.sh' in the installation di‐
888 rectory. (default: None)
889 --jobname NAME, --jn NAME
891 Provide a custom name for the jobscript that is submitted to the
892 cluster (see --cluster). NAME is "snakejob.{name}.{jobid}.sh"
893 per default. The wildcard {jobid} has to be present in the name.
894 (default: snakejob.{name}.{jobid}.sh)
895 --cluster-status CLUSTER_STATUS
897 Status command for cluster execution. This is only considered in
898 combination with the --cluster flag. If provided, Snakemake will
899 use the status command to determine if a job has finished suc‐
900 cessfully or failed. For this it is necessary that the submit
901 command provided to --cluster returns the cluster job id. Then,
902 the status command will be invoked with the job id. Snakemake
903 expects it to return 'success' if the job was successful,
904 'failed' if the job failed and 'running' if the job still runs.
905 (default: None)
906 --cluster-cancel CLUSTER_CANCEL
908 Specify a command that allows to stop currently running jobs.
909 The command will be passed a single argument, the job id. (de‐
910 fault: None)
911 --cluster-cancel-nargs CLUSTER_CANCEL_NARGS
913 Specify maximal number of job ids to pass to --cluster-cancel
914 command, defaults to 1000. (default: 1000)
915 --cluster-sidecar CLUSTER_SIDECAR
917 Optional command to start a sidecar process during cluster exe‐
918 cution. Only active when --cluster is given as well. (default:
919 None)
920 --drmaa-log-dir DIR
922 Specify a directory in which stdout and stderr files of DRMAA
923 jobs will be written. The value may be given as a relative path,
924 in which case Snakemake will use the current invocation direc‐
925 tory as the origin. If given, this will override any given '-o'
926 and/or '-e' native specification. If not given, all DRMAA stdout
927 and stderr files are written to the current working directory.
928 (default: None)
929 FLUX:
931 --flux Execute your workflow on a flux cluster. Flux can work with both
932 a shared network filesystem (like NFS) or without. If you don't
933 have a shared filesystem, additionally specify --no-shared-fs.
934 (default: False)
935 GOOGLE_LIFE_SCIENCE:
937 --google-lifesciences
938 Execute workflow on Google Cloud cloud using the Google Life.
939 Science API. This requires default application credentials
940 (json) to be created and export to the environment to use Google
941 Cloud Storage, Compute Engine, and Life Sciences. The credential
942 file should be exported as GOOGLE_APPLICATION_CREDENTIALS for
943 snakemake to discover. Also, --use-conda, --usesingularity,
944 --config, --configfile are supported and will be carried over.
945 (default: False)
946 --google-lifesciences-regions GOOGLE_LIFESCIENCES_REGIONS [GOOGLE_LIFE‐
948 SCIENCES_REGIONS ...]
949 Specify one or more valid instance regions (defaults to US) (de‐
950 fault: ['us-east1', 'us-west1', 'uscentral1'])
951 --google-lifesciences-location GOOGLE_LIFESCIENCES_LOCATION
953 The Life Sciences API service used to schedule the jobs. E.g.,
954 us-centra1 (Iowa) and europe-west2 (London) Watch the terminal
955 output to see all options found to be available. If not speci‐
956 fied, defaults to the first found with a matching prefix from
957 regions specified with --google-lifesciences-regions. (default:
958 None)
959 --google-lifesciences-keep-cache
961 Cache workflows in your Google Cloud Storage Bucket specified by
962 --default-remote-prefix/{source}/{cache}. Each workflow working
963 directory is compressed to a .tar.gz, named by the hash of the
964 contents, and kept in Google Cloud Storage. By default, the
965 caches are deleted at the shutdown step of the workflow. (de‐
966 fault: False)
967 --google-lifesciences-service-account-email GOOGLE_LIFESCIENCES_SER‐
969 VICE_ACCOUNT_EMAIL
970 Specify a service account email address (default: None)
971 --google-lifesciences-network GOOGLE_LIFESCIENCES_NETWORK
973 Specify a network for a Google Compute Engine VM instance (de‐
974 fault: None)
975 --google-lifesciences-subnetwork GOOGLE_LIFESCIENCES_SUBNETWORK
977 Specify a subnetwork for a Google Compute Engine VM instance
978 (default: None)
979 KUBERNETES:
981 --kubernetes [NAMESPACE]
982 Execute workflow in a kubernetes cluster (in the cloud). NAME‐
983 SPACE is the namespace you want to use for your job (if nothing
984 specified: 'default'). Usually, this requires --default-re‐
985 mote-provider and --defaultremote-prefix to be set to a S3 or GS
986 bucket where your . data shall be stored. It is further advis‐
987 able to activate conda integration via --use-conda. (default:
988 None)
989 --container-image IMAGE
991 Docker image to use, e.g., when submitting jobs to kubernetes
992 Defaults to 'https://hub.docker.com/r/snakemake/snakemake',
993 tagged with the same version as the currently running Snakemake
994 instance. Note that overwriting this value is up to your respon‐
995 sibility. Any used image has to contain a working snakemake in‐
996 stallation that is compatible with (or ideally the same as) the
997 currently running version. (default: None)
998 --k8s-cpu-scalar FLOAT
1000 K8s reserves some proportion of available CPUs for its own use.
1001 So, where an underlying node may have 8 CPUs, only e.g. 7600
1002 milliCPUs are allocatable to k8s pods (i.e. snakemake jobs). As
1003 8 > 7.6, k8s can't find a node with enough CPU resource to run
1004 such jobs. This argument acts as a global scalar on each job's
1005 CPU request, so that e.g. a job whose rule definition asks for 8
1006 CPUs will request 7600m CPUs from k8s, allowing it to utilise
1007 one entire node. N.B: the job itself would still see the origi‐
1008 nal value, i.e. as the value substituted in {threads}. (default:
1009 0.95)
1010 --k8s-service-account-name SERVICEACCOUNTNAME
1012 This argument allows the use of customer service accounts for
1013 kubernetes pods. If specified serviceAccountName will be added
1014 to the pod specs. This is needed when using workload identity
1015 which is enforced when using Google Cloud GKE Autopilot. (de‐
1016 fault: None)
1017 TES:
1019 --tes URL
1020 Send workflow tasks to GA4GH TES server specified by url. (de‐
1021 fault: None)
1022 TIBANNA:
1024 --tibanna
1025 Execute workflow on AWS cloud using Tibanna. This requires --de‐
1026 fault-remote-prefix to be set to S3 bucket name and prefix (e.g.
1027 'bucketname/subdirectory') where input is already stored and
1028 output will be sent to. Using --tibanna implies --default-re‐
1029 sources is set as default. Optionally, use --precommand to
1030 specify any preparation command to run before snakemake command
1031 on the cloud (inside snakemake container on Tibanna VM). Also,
1032 --use-conda, --use-singularity, --config, --configfile are sup‐
1033 ported and will be carried over. (default: False)
1034 --tibanna-sfn TIBANNA_SFN
1036 Name of Tibanna Unicorn step function (e.g. tibanna_uni‐
1037 corn_monty). This works as serverless scheduler/resource alloca‐
1038 tor and must be deployed first using tibanna cli. (e.g. tibanna
1039 deploy_unicorn --usergroup=monty --buckets=bucketname) (default:
1040 None)
1041 --precommand PRECOMMAND
1043 Any command to execute before snakemake command on AWS cloud
1044 such as wget, git clone, unzip, etc. This is used with
1045 --tibanna.Do not include input/output download/upload commands -
1046 file transfer between S3 bucket and the run environment (con‐
1047 tainer) is automatically handled by Tibanna. (default: None)
1048 --tibanna-config TIBANNA_CONFIG [TIBANNA_CONFIG ...]
1050 Additional tibanna config e.g. --tibanna-config spot_in‐
1051 stance=true subnet=<subnet_id> security group=<secu‐
1052 rity_group_id> (default: None)
1053 AZURE_BATCH:
1055 --az-batch
1056 Execute workflow on azure batch (default: False)
1057 --az-batch-enable-autoscale
1059 Enable autoscaling of the azure batch pool nodes, this option
1060 will set the initial dedicated node count to zero, and requires
1061 five minutes to resize the cluster, so is only recommended for
1062 longer running jobs. (default: False)
1063 --az-batch-account-url [AZ_BATCH_ACCOUNT_URL]
1065 Azure batch account url, requires AZ_BATCH_ACCOUNT_KEY environ‐
1066 ment variable to be set. (default: None)
1067 CONDA:
1069 --use-conda
1070 If defined in the rule, run job in a conda environment. If this
1071 flag is not set, the conda directive is ignored. (default:
1072 False)
1073 --conda-not-block-search-path-envvars
1075 Do not block environment variables that modify the search path
1076 (R_LIBS, PYTHONPATH, PERL5LIB, PERLLIB) when using conda envi‐
1077 ronments. (default: False)
1078 --list-conda-envs
1080 List all conda environments and their location on disk. (de‐
1081 fault: False)
1082 --conda-prefix DIR
1084 Specify a directory in which the 'conda' and 'condaarchive' di‐
1085 rectories are created. These are used to store conda environ‐
1086 ments and their archives, respectively. If not supplied, the
1087 value is set to the '.snakemake' directory relative to the invo‐
1088 cation directory. If supplied, the `--use-conda` flag must also
1089 be set. The value may be given as a relative path, which will be
1090 extrapolated to the invocation directory, or as an absolute
1091 path. The value can also be provided via the environment vari‐
1092 able $SNAKEMAKE_CONDA_PREFIX. (default: None)
1093 --conda-cleanup-envs
1095 Cleanup unused conda environments. (default: False)
1096 --conda-cleanup-pkgs [{tarballs,cache}]
1098 Cleanup conda packages after creating environments. In case of
1099 'tarballs' mode, will clean up all downloaded package tarballs.
1100 In case of 'cache' mode, will additionally clean up unused pack‐
1101 age caches. If mode is omitted, will default to only cleaning up
1102 the tarballs. (default: None)
1103 --conda-create-envs-only
1105 If specified, only creates the job-specific conda environments
1106 then exits. The `--use-conda` flag must also be set. (default:
1107 False)
1108 --conda-frontend {conda,mamba}
1110 Choose the conda frontend for installing environments. Mamba is
1111 much faster and highly recommended. (default: mamba)
1112 SINGULARITY:
1114 --use-singularity
1115 If defined in the rule, run job within a singularity container.
1116 If this flag is not set, the singularity directive is ignored.
1117 (default: False)
1118 --singularity-prefix DIR
1120 Specify a directory in which singularity images will be stored.
1121 If not supplied, the value is set to the '.snakemake' directory
1122 relative to the invocation directory. If supplied, the
1123 `--use-singularity` flag must also be set. The value may be
1124 given as a relative path, which will be extrapolated to the in‐
1125 vocation directory, or as an absolute path. (default: None)
1126 --singularity-args ARGS
1128 Pass additional args to singularity. (default: )
1129 --cleanup-containers
1131 Remove unused (singularity) containers (default: False)
1132 ENVIRONMENT MODULES:
1134 --use-envmodules
1135 If defined in the rule, run job within the given environment
1136 modules, loaded in the given order. This can be combined with
1137 --use-conda and --usesingularity, which will then be only used
1138 as a fallback for rules which don't define environment modules.
1139 (default: False)
1140 If an arg is specified in more than one place, then commandline
1142 values
1143 override environment variables which override defaults.
1145snakemake 7.32.4 September 2023 SNAKEMAKE(1)