CLI Reference

Show per-tool CLI options with --help <tool>:

./cpipes --pipeline maggic --help

Available Tool Help

Flag	Tool
--help fastp	fastp quality filtering options
--help filtlong	Filtlong quality filtering options (maggic_lr)
--help megahit	MEGAHIT assembly options
--help flye	Flye assembly options (maggic_lr)
--help minimap2	Minimap2 alignment options
--help seb	SemiBin2 single_easy_bin options
--help vamb	VAMB bin def options
--help binette	Binette consensus binning options
--help gtdbtk	GTDB-Tk classify_wf options
--help abundance	CoverM genome coverage options
--help amrfinderplus	AMRFinderPlus profiling options
--help metabat2	MetaBAT 2 binning options

Examples

# Show all tool help flags (short-read)
./cpipes --pipeline maggic --help

# Show all tool help flags (long-read)
./cpipes --pipeline maggic_lr --help

# Show fastp options (short-read only)
./cpipes --pipeline maggic --help fastp

# Show filtlong options (long-read only)
./cpipes --pipeline maggic_lr --help filtlong

# Show multiple tools
./cpipes --pipeline maggic --help fastp,megahit
./cpipes --pipeline maggic_lr --help filtlong,flye

Full Help Output

./cpipes --pipeline maggic --help

N E X T F L O W   ~  version 25.10.5

Launching `./cpipes` [distracted_panini] DSL2 - revision: 0a03b0b454

====================================================================================================             (o)
  ___  _ __   _  _ __    ___  ___
 / __|| '_ \ | || '_ \  / _ \/ __|
| (__ | |_) || || |_) ||  __/\__ \
 \___|| .__/ |_|| .__/  \___||___/
      | |       | |
      |_|       |_|
----------------------------------------------------------------------------------------------------
A collection of modular pipelines at CFSAN, FDA.
----------------------------------------------------------------------------------------------------
Name                                                   : CPIPES
Author                                                 : Kranti.Konganti@fda.hhs.gov
Version                                                : 0.9.0
Center                                                 : CFSAN, FDA.
====================================================================================================

----------------------------------------------------------------------------------------------------
Show configurable CLI options for each tool within maggic
----------------------------------------------------------------------------------------------------
Ex: cpipes --pipeline maggic --help
Ex: cpipes --pipeline maggic --help fastp
Ex: cpipes --pipeline maggic --help fastp,megahit
----------------------------------------------------------------------------------------------------
--help fastp                                           : Show fastp CLI options (maggic only)
--help filtlong                                        : Show filtlong CLI options (maggic_lr only)
--help megahit                                         : Show megahit CLI options (maggic only)
--help flye                                            : Show flye CLI options (maggic_lr only)
--help minimap2                                        : Show minimap2 CLI options
--help seb                                             : Show SemiBin2 `single_easy_bin` CLI options
--help vamb                                            : Show vamb `bin def` CLI options
--help binette                                         : Show binette CLI options
--help gtdbtk                                          : Show gtdbtk classify_wf CLI options
--help abundance                                       : Show CoverM `genome` CLI options
--help amrfinderplus                                   : Show AMRFinderPlus CLI options
--help metabat2                                        : Show metabat2 CLI options