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

Path to a comma-separated file (CSV) listing samples to process. Must contain a header with two columns: ‘id’ (sample identifier) and ‘raw_file’ (full path to the corresponding RAW file). You may specify one or multiple samples for batch processing.

required
type: string
pattern: ^\S+\.csv$

Directory where the pipeline will write its output. If a relative folder name is used (e.g., ‘results’), it will be created in the current working directory. If an absolute path is given (e.g., ‘/path/to/output’), the folder will be created at that specific location.

required
type: string

Email address for completion summary.

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

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

Incoming hook URL for messaging service

hidden
type: string

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

Parameters used for chromatographic peak extraction and visualisation

Path to a tab-separated values (TSV) file describing the analytes for chromatographic peak extraction. Must include columns: short_name, long_name, mz_M0 (required), and optionally mz_M1, mz_M2, ms2_mz, and rt_teoretical (required). Only mz_M0 and rt_teoretical are mandatory. mz_M1 and mz_M2 are reserved for future support of isotopic envelope integration.

required
type: string
pattern: ^\S+\.tsv$

Short name of the analyte to be extracted, as defined in the ‘short_name’ column of the TSV file. Use a specific value such as ‘m3C’ to process one analyte, or use ‘all’ to process all analytes defined in the TSV file.

required
type: string

Time window (in seconds) around the theoretical retention time in which peaks will be searched. The window is defined as RT ± tolerance.

required
type: integer
default: 150

Tolerance in parts-per-million (ppm) around the specified precursor m/z value (mz_M0) for XIC extraction. The window is defined as mz_M0 ± tolerance.

required
type: integer
default: 20

MS level to extract chromatographic peaks from. Set to 1 for MS1 or 2 for MS2.

required
type: integer
default: 2

Whether to plot MS1 XICs

type: boolean

Whether to plot MS2 XICs

type: boolean

Output file name for the XIC PDF plot

type: string
default: xic_plot.pdf

Whether to generate an additional TSV file accumulating the XIC extraction results. If set to true, the output will include a progressively updated results table based on the original input analytes TSV.

type: boolean