NAME

       PiGx - pipeline to interpret high-throughput RNA sequencing data

DESCRIPTION

       usage: pigx-rnaseq [-h] [-v]

              (--init  [{settings,sample-sheet,both}]  |  -s  SETTINGS)  [-c  CONFIGFILE] [--target TARGET] [-n]
              [--graph GRAPH] [--force] [--reason] [--unlock] [sample_sheet]

       PiGx RNAseq Pipeline.

       PiGx RNAseq is a data processing pipeline for RNAseq read data.

   positional arguments:
       sample_sheet
              The sample sheet containing sample data in CSV format.

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

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

       --init [{settings,sample-sheet,both}]
              Generate a template SETTINGS file, a SAMPLE-SHEET.  Leave empty for both.

       -s SETTINGS, --settings SETTINGS
              A YAML file for settings that deviate from the defaults.

       -c CONFIGFILE, --configfile CONFIGFILE
              The config file  used  for  calling  the  underlying  snakemake  process.   By  default  the  file
              'config.json' is dynamically created from the sample sheet and the settings file.

       --target TARGET
              Stop when the named target is completed instead of running the whole pipeline.  The default target
              is "final-report".  Pass "--target=help" to describe all available targets.

       -n, --dry-run
              Only show what work would be performed.  Do not actually run the pipeline.

       --graph GRAPH
              Output  a  graph in Graphviz dot format showing the relations between rules of this pipeline.  You
              must specify a graph file name such as "graph.pdf".

       --force
              Force the execution of rules, even though the outputs are considered fresh.

       --reason
              Print the reason why a rule is executed.

       --unlock
              Recover after a snakemake crash.

       This pipeline was developed by the Akalin group at MDC in Berlin in 2017-2018.

       Version: 0.0.9

COPYRIGHT

       Copyright ?? 2017, 2018 Bora Uyar, Jona Ronen, Ricardo Wurmus.  License GPLv3+:  GNU  GPL  version  3  or
       later <http://gnu.org/licenses/gpl.html>.

       This  is  free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent
       permitted by law.

SEE ALSO

       The full documentation for PiGx

PiGx RNAseq Pipeline.                            September 2020                                          PIGX(1)