---
name: "pigx-rnaseq"
section: "1"
platform: "linux"
package: "pigx-rnaseq"
version: "0.1.1-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pigx-rnaseq"
---

# pigx-rnaseq(1)

pipeline to interpret high-throughput RNA sequencing data

## 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**