PIGX(1)

📦
version 0.1.1 · 2 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

PIGX(1) 💖

User Commands ✨ (it's the man page for PiGx, bestie, and yes we're doing the whole thing)

🌸 NAME 🌸

PiGx — a pipeline to interpret high-throughput RNA sequencing data 🧬✨

🎀 DESCRIPTION 🎀

okay so first things first, here's the usage, and I need you to read it exactly like this, no vibes-based paraphrasing:

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. Like, that's the whole point. It takes your reads and it processes them. Iconic behaviour, honestly.

🦋 positional arguments 🦋

  • sample_sheet — the sample sheet containing sample data in CSV format. Yes bestie, CSV, comma-separated, you know the drill 📄

✨ optional arguments ✨

  • -h, --help — shows this help message and dips. 👋
  • -v, --version — shows the program's version number and exits. Quick little flex. 💁
  • --init [{settings,sample-sheet,both}] — generates a template SETTINGS file, a SAMPLE-SHEET, or both. Leave it empty and you get both. Two for one, we love a bargain. 🎁
  • -s SETTINGS, --settings SETTINGS — a YAML file for settings that deviate from the defaults. Your little customisation era. 💅
  • -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. ✨ (yes, dynamically, she's built different)
  • --target TARGET — stop when the named target is completed instead of running the whole pipeline. The default target is "final-report". And if you pass "--target=help" it will describe all available targets for you. 🎯
  • -n, --dry-run — only show what work would be performed. Do not actually run the pipeline. Window shopping only, no purchasing. 🛍️
  • --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. She's stubborn, respect it. 💪
  • --reason — print the reason why a rule is executed. Receipts! 🧾
  • --unlock — recover after a snakemake crash. The "we don't talk about what happened here" option. 😭🫶
This pipeline was developed by the Akalin group at MDC in Berlin in 2017-2018. 🏛️
Version: 0.0.9 ⭐

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 📚

okay that's the whole page bestie, you ate that 🍓

signing off from the PiGx RNAseq Pipeline man page, September 2020, filed under PIGX(1) — mwah 💋

📦 where this page comes from