PiGx - pipeline to interpret high-throughput RNA sequencing data

       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.

       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.

   positionalarguments:
       sample_sheet
              The sample sheet containing sample data in CSV format.

   optionalarguments:-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

       PiGx - pipeline to interpret high-throughput RNA sequencing data

       The full documentation for PiGx

PiGx RNAseq Pipeline.                            September 2020                                          PIGX(1)