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