Introduction Usage Parameters Output Releases

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

Path to input data file(s) (globs must be surrounded with quotes). Currently supported formats are *.mcd, *.ome.tiff, *.txt.

required
type: string
default: data/*.mcd

Path to metadata csv file indicating which images to merge in full stack and/or Ilastik stack.

required
type: string
default: ./metadata.csv

CellProfiler pipeline file required to create full stack (cppipe format).

required
type: string

CellProfiler pipeline file required to create Ilastik stack (cppipe format).

required
type: string

CellProfiler pipeline file required for segmentation (cppipe format).

required
type: string

Parameter file required by Ilastik (ilp format).

type: string

Tiff file for compensation analysis during CellProfiler preprocessing steps.

type: string

Path to directory with plugin files required for CellProfiler.

type: string
default: $projectDir/assets/plugins

Tiff file for compensation analysis during CellProfiler preprocessing steps.

type: boolean

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})$

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

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|day)\s*)+$

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

Display help text.

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

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.

hidden
type: boolean
On this page