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

Use this to specify the location of your input files. For example:

--input 'path/to/data/*.mcd'

Please note the following requirements:

  1. The path must be enclosed in quotes
  2. The path must have at least one * wildcard character

If left unspecified, a default pattern is used: 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

The file should only contain 3 columns i.e. 'metal', 'full_stack' and 'ilastik_stack'. The metal column should contain all the metals used in your antibody panel. The full_stack and ilastik_stack entries should be 1 or 0 to indicate whether to include or exclude a metal for a given stack, respectively. See metadata.csv for an example.

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})$

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

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

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

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

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

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$

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

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*)+$

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

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

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

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})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

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

By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.

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

hidden
type: boolean
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