Introduction Usage Parameters Output

Define where the pipeline should find input data and save output data.

Path to phyloseq RDS file containing OTU table, taxonomy, sample metadata.

required
type: string

Path to control-only phyloseq RDS (optional). If null and simulate=true, extracted from input.

type: string

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Choose between real-only consensus (Path A) and simulation-trained weighted consensus (Path B).

Enable simulation mode (Path B). Set to false for real-only k-intersection (Path A).

type: boolean
default: true

Metadata column names for real data analysis and control extraction.

sample_data column with the group variable (case vs control).

type: string
default: study_condition

Reference/control level in the condition column.

type: string
default: healthy

Optional confounder column(s) in sample_data.

type: string

Batch-correction confounder column (used by Maaslin2).

type: string

Condition column name for simulated data (set by MIDASim, usually ‘group’).

hidden
type: string
default: group

Base level name for simulated data (set by MIDASim, usually ‘control’).

hidden
type: string
default: control

Confounder column for simulated data analysis.

hidden
type: string

Batch-correction confounder for simulated data.

hidden
type: string

Parameters controlling the MIDASim simulation grid (Path B only).

Number of control samples per simulation. If null, uses input dataset size.

type: integer

Number of case samples per simulation. If null, uses input dataset size.

type: integer

Proportions of DA taxa to simulate (Nextflow list, e.g. [0.05, 0.10]).

type: string

Absolute log-fold changes to simulate (Nextflow list, e.g. [0.5, 1.0, 2.0]).

type: string

Number of replicates per scenario.

type: integer
default: 3

Sample design types to simulate (Nextflow list, e.g. [balanced, unbalanced]).

type: string

Optional sample_data column to subset controls before simulation.

type: string

Level to keep when subsetting controls.

type: string

Optional batch column for batch-aware simulation.

type: string

Standard deviation for batch effects.

type: number
default: 0.3

Base random seed for simulations.

type: integer
default: 123

Prefix for scenario folder names.

type: string
default: dataset

Output directory for simulated data.

hidden
type: string

Toggle which differential abundance tools to run.

Run ADAPT.

type: boolean
default: true

Run corncob.

type: boolean
default: true

Run LinDA (MicrobiomeStat).

type: boolean
default: true

Run LOCOM2.

type: boolean
default: true

Run Maaslin2.

type: boolean
default: true

Run metagenomeSeq.

type: boolean

Contrast mode for metagenomeSeq.

type: string

Contrast specification for metagenomeSeq.

type: string

Parameters for DA scoring (Path B) and k-intersection consensus (Path A).

Significance threshold for DA evaluation.

type: number
default: 0.05

Target FDR for scoring.

type: number
default: 0.05

Reference FDR threshold for scoring.

type: number
default: 0.1

Minimum retention at reference FDR.

type: number
default: 0.25

Significance threshold for k-intersection consensus (Path A).

type: number
default: 0.05

Minimum log-fold change for k-intersection consensus (Path A).

type: number

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Less common options for the pipeline, typically set in a config file.

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

Do not use coloured log outputs.

hidden
type: boolean

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden
type: string

Display the help message.

type: boolean,string

Display the full detailed help message.

type: boolean

Display hidden parameters in the help message (only works when –help or –help_full are provided).

type: boolean
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