Provided by: snakemake_5.4.0-1_all bug

NAME

       snakemake - a Python based language and execution environment for GNU Makelike workflows

DESCRIPTION

       usage: snakemake [-h] [--snakefile FILE] [--gui [PORT]] [--cores [N]]

              [--resources  [NAME=INT  [NAME=INT  ...]]]   [--config [KEY=VALUE [KEY=VALUE ...]]]
              [--configfile FILE] [--list]  [--list-target-rules]  [--directory  DIR]  [--dryrun]
              [--printshellcmds] [--dag] [--rulegraph] [--d3dag] [--summary] [--detailed-summary]
              [--touch] [--keep-going] [--force] [--forceall] [--forcerun  TARGET  [TARGET  ...]]
              [--prioritize   TARGET   [TARGET   ...]]   [--allow-ambiguity]   [--cluster  CMD  |
              --cluster-sync CMD | --drmaa [ARGS]] [--cluster-config  FILE]  [--immediate-submit]
              [--jobscript   SCRIPT]  [--jobname  NAME]  [--reason]  [--stats  FILE]  [--nocolor]
              [--quiet]   [--nolock]   [--unlock]   [--cleanup-metadata   [FILE   [FILE    ...]]]
              [--rerun-incomplete]         [--ignore-incomplete]         [--list-version-changes]
              [--list-code-changes]        [--list-input-changes]         [--list-params-changes]
              [--latency-wait  SECONDS] [--wait-for-files [FILE [FILE ...]]] [--benchmark-repeats
              N] [--notemp] [--keep-target-files] [--allowed-rules  ALLOWED_RULES  [ALLOWED_RULES
              ...]]      [--timestamp]     [--greediness     GREEDINESS]    [--print-compilation]
              [--overwrite-shellcmd OVERWRITE_SHELLCMD] [--verbose]  [--debug]  [--profile  FILE]
              [--bash-completion] [--version] [target [target ...]]

   positional arguments:
       target Targets to build. May be rules or files.

   optional arguments:
       -h, --help
              show this help message and exit

       --snakefile FILE, -s FILE
              The workflow definition in a snakefile.

       --gui [PORT]
              Serve  an HTML based user interface to the given port (default: 8000). If possible,
              a browser window is opened.

       --cores [N], --jobs [N], -j [N]
              Use at most N cores in parallel (default: 1). If N is omitted, the limit is set  to
              the number of available cores.

       --resources [NAME=INT [NAME=INT ...]], --res [NAME=INT [NAME=INT ...]]
              Define  additional  resources  that  shall  constrain the scheduling analogously to
              threads (see above). A resource is defined as a name and an  integer  value.   E.g.
              --resources  gpu=1.  Rules can use resources by defining the resource keyword, e.g.
              resources: gpu=1.  If now two rules require 1 of the resource 'gpu' they  won't  be
              run in parallel by the scheduler.

       --config [KEY=VALUE [KEY=VALUE ...]]
              Set  or overwrite values in the workflow config object.  The workflow config object
              is accessible as variable config inside the workflow. Default values can be set  by
              providing a JSON file (see Documentation).

       --configfile FILE
              Specify  or  overwrite  the  config  file  of  the  workflow (see the docs). Values
              specified in JSON or YAML format are available  in  the  global  config  dictionary
              inside the workflow.

       --list, -l
              Show available rules in given Snakefile.

       --list-target-rules, --lt
              Show available target rules in given Snakefile.

       --directory DIR, -d DIR
              Specify  working  directory (relative paths in the snakefile will use this as their
              origin).

       --dryrun, -n
              Do not execute anything.

       --printshellcmds, -p
              Print out the shell commands that will be executed.

       --dag  Do not execute anything and print the directed acyclic graph of  jobs  in  the  dot
              language. Recommended use on Unix systems: snakemake --dag | dot | display

       --rulegraph
              Do  not  execute  anything  and  print  the  dependency  graph  of rules in the dot
              language. This will be less crowded than above DAG of  jobs,  but  also  show  less
              information.  Note that each rule is displayed once, hence the displayed graph will
              be cyclic if a rule appears in several steps of the workflow.  Use  this  if  above
              option  leads  to  a  DAG  that  is  too  large.   Recommended use on Unix systems:
              snakemake --rulegraph | dot | display

       --d3dag
              Print the DAG in D3.js compatible JSON format.

       --summary, -S
              Print a summary of all files created  by  the  workflow.   The  has  the  following
              columns:  filename,  modification  time,  rule  version, status, plan. Thereby rule
              version contains the versionthe file was created with (see the version  keyword  of
              rules),  and  status denotes whether the file is missing, its input files are newer
              or if version or implementation of the rule changed since  file  creation.  Finally
              the last column denotes whether the file will be updated or created during the next
              workflow execution.

       --detailed-summary, -D
              Print a summary of all files created  by  the  workflow.   The  has  the  following
              columns:  filename,  modification time, rule version, input file(s), shell command,
              status, plan. Thereby rule version contains the versionthe file  was  created  with
              (see the version keyword of rules), and status denotes whether the file is missing,
              its input files are newer or if version or implementation of the rule changed since
              file  creation.  The  input  file  and  shell  command columns are selfexplanatory.
              Finally the last column denotes whether the file will be updated or created  during
              the next workflow execution.

       --touch, -t
              Touch  output  files (mark them up to date without really changing them) instead of
              running their commands. This is used to pretend that the rules  were  executed,  in
              order to fool future invocations of snakemake. Fails if a file does not yet exist.

       --keep-going, -k
              Go on with independent jobs if a job fails.

       --force, -f
              Force  the execution of the selected target or the first rule regardless of already
              created output.

       --forceall, -F
              Force the execution of the selected (or  the  first)  rule  and  all  rules  it  is
              dependent on regardless of already created output.

       --forcerun TARGET [TARGET ...], -R TARGET [TARGET ...]
              Force  the re-execution or creation of the given rules or files. Use this option if
              you changed a rule and want to have all its output in your workflow updated.

       --prioritize TARGET [TARGET ...], -P TARGET [TARGET ...]
              Tell the scheduler to assign creation of given targets (and all their dependencies)
              highest priority.  (EXPERIMENTAL)

       --allow-ambiguity, -a
              Don't check for ambiguous rules and simply use the first if several can produce the
              same file. This allows  the  user  to  prioritize  rules  by  their  order  in  the
              snakefile.

       --cluster CMD, -c CMD
              Execute  snakemake  rules  with  the  given  submit  command,  e.g. qsub. Snakemake
              compiles jobs into scripts that  are  submitted  to  the  cluster  with  the  given
              command, once all input files for a particular job are present.  The submit command
              can be decorated to make it aware of certain job properties (input, output, params,
              wildcards,  log,  threads  and  dependencies  (see  the  argument  below)), e.g.: $
              snakemake --cluster 'qsub -pe threaded {threads}'.

       --cluster-sync CMD
              cluster submission command will block, returning the remote exitstatus upon  remote
              termination  (for example, this should be usedif the cluster command is 'qsub -sync
              y' (SGE)

       --drmaa [ARGS]
              Execute snakemake on a cluster accessed via DRMAA,  Snakemake  compiles  jobs  into
              scripts  that  are  submitted to the cluster with the given command, once all input
              files for a particular job are present. ARGS can be used to specify options of  the
              underlying  cluster system, thereby using the job properties input, output, params,
              wildcards, log, threads and dependencies, e.g.: --drmaa ' -pe threaded  {threads}'.
              Note that ARGS must be given in quotes and with a leading whitespace.

       --cluster-config FILE, -u FILE
              A JSON or YAML file that defines the wildcards used in 'cluster'for specific rules,
              instead of having them specified in the Snakefile.For example, for rule  'job'  you
              may define: { 'job' : { 'time' : '24:00:00' } } to specify the time for rule 'job'.

       --immediate-submit, --is
              Immediately  submit  all  jobs  to the cluster instead of waiting for present input
              files. This will fail, unless you make the cluster aware of job dependencies,  e.g.
              via:  $ snakemake --cluster 'sbatch --dependency {dependencies}. Assuming that your
              submit script (here sbatch) outputs the generated job id to the first stdout  line,
              {dependencies} will be filled with space separated job ids this job depends on.

       --jobscript SCRIPT, --js SCRIPT
              Provide  a  custom  job  script  for  submission to the cluster. The default script
              resides as 'jobscript.sh' in the installation directory.

       --jobname NAME, --jn NAME
              Provide a custom name for the jobscript that  is  submitted  to  the  cluster  (see
              --cluster).  NAME  is  "snakejob.{rulename}.{jobid}.sh"  per  default. The wildcard
              {jobid} has to be present in the name.

       --reason, -r
              Print the reason for each executed rule.

       --stats FILE
              Write stats about Snakefile execution in JSON format to the given file.

       --nocolor
              Do not use a colored output.

       --quiet, -q
              Do not output any progress or rule information.

       --nolock
              Do not lock the working directory

       --unlock
              Remove a lock on the working directory.

       --cleanup-metadata [FILE [FILE ...]], --cm [FILE [FILE ...]]
              Cleanup the metadata of given files. That means that snakemake removes any  tracked
              version info, and any marks that files are incomplete.

       --rerun-incomplete, --ri
              Re-run all jobs the output of which is recognized as incomplete.

       --ignore-incomplete, --ii
              Ignore any incomplete jobs.

       --list-version-changes, --lv
              List  all  output  files  that  have  been  created  with  a  different version (as
              determined by the version keyword).

       --list-code-changes, --lc
              List all output files for which the rule body (run or shell) have  changed  in  the
              Snakefile.

       --list-input-changes, --li
              List  all  output  files  for  which  the  defined  input files have changed in the
              Snakefile (e.g. new input files were added in the rule  definition  or  files  were
              renamed). For listing input file modification in the filesystem, use --summary.

       --list-params-changes, --lp
              List all output files for which the defined params have changed in the Snakefile.

       --latency-wait SECONDS, --output-wait SECONDS, -w SECONDS
              Wait  given  seconds  if  an  output  file  of  a  job is not present after the job
              finished. This helps if your filesystem suffers from latency (default 5).

       --wait-for-files [FILE [FILE ...]]
              Wait --latency-wait seconds for these files to  be  present  before  executing  the
              workflow.  This  option  is used internally to handle filesystem latency in cluster
              environments.

       --benchmark-repeats N
              Repeat a job N times if marked for benchmarking (default 1).

       --notemp, --nt
              Ignore temp() declarations. This  is  useful  when  running  only  a  part  of  the
              workflow,  since  temp()  would  lead to deletion of probably needed files by other
              parts of the workflow.

       --keep-target-files
              Do not adjust the paths of given target files relative to the working directory.

       --allowed-rules ALLOWED_RULES [ALLOWED_RULES ...]
              Only use given rules. If omitted, all rules in Snakefile are used.

       --timestamp, -T
              Add a timestamp to all logging output

       --greediness GREEDINESS
              Set the greediness of scheduling. This value between 0 and 1 determines how careful
              jobs  are  selected  for execution. The default value (1.0) provides the best speed
              and still acceptable scheduling quality.

       --print-compilation
              Print the python representation of the workflow.

       --overwrite-shellcmd OVERWRITE_SHELLCMD
              Provide a shell command that shall be  executed  instead  of  those  given  in  the
              workflow. This is for debugging purposes only.

       --verbose
              Print debugging output.

       --debug
              Allow  one to debug rules with e.g. PDB. This flag allows to set breakpoints in run
              blocks.

       --profile FILE
              Profile Snakemake and  write  the  output  to  FILE.  This  requires  yappi  to  be
              installed.

       --bash-completion
              Output  code  to register bash completion for snakemake.  Put the following in your
              .bashrc (including the accents): `snakemake --bash-completion` or issue  it  in  an
              open terminal session.

       --version, -v
              show program's version number and exit