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

Path to comma-separated file containing information about the samples in the experiment.

required
type: string
pattern: ^\S+\.(csv|tsv)$

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.

Path to a local or remote directory that is the "current working directory" for relative paths defined in the input samplesheet

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})$

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.

Trim N bases from the front of the reads

type: integer

Trim N bases from the tail of the reads

type: integer

The maximum length of a read

type: integer

Reads longer then given length will be trimmed to the given length. If you set this argument it will overrule the value from the chosen design

The minimum length (bases) of a read

type: integer

Reads shorter then given length will be discarded. If you set this argument it will overrule the value from the chosen design.

The maximum number of Ns allowed in a read

type: integer

The default value of 0 means any reads with N in it will be filtered out

Minimum avg. quality a read must have (0 will disable the filter)

type: integer
default: 20

Remove duplicated reads (exact same sequence)

type: boolean

Remove PolyG sequences (length of 10 or more)

type: boolean

The number of mismatches allowed (in percentage) [default: 0.1; 0.0<=x<=0.9]

type: number
default: 0.1

The number of mismatches allowed (as a fraction)

type: number
default: 0.1

The minimum length of the barcode that must overlap when matching

type: integer

If you set this argument it will overrule the value from the chosen design

A list of comma separated antibodies to discard

type: string
pattern: (\S+)?(,\S+)*

The algorithm to use for collapsing (adjacency will perform error correction using the number of mismatches given)

type: string

The maximum number of neighbors to use when searching for similar sequences. This number depends on the sequence depth and the ratio of erroneous molecules expected. A high value can make the algorithm slower. This is only used when algorithm is set to 'adjacency'

hidden
type: integer
default: 60

The number of mismatches allowed when collapsing (adjacency)

type: integer
default: 2

Discard molecules with with a count (reads) lower than this value

type: integer
default: 2

Use counts when collapsing (the difference in counts between two molecules must be more than double in order to be collapsed)

type: boolean

Activate the multiplet recovery using leiden community detection

type: boolean
default: true

Number of iterations for the leiden algorithm, high values will decrease the variance of the results but increase the runtime [default: 10; 1<=x<=100]

hidden
type: integer
default: 10

Discard edges (pixels) with a count (reads) lower than this, use 1 to disable

hidden
type: integer
default: 2

The minimum size (pixels) a component/cell can have (disabled by default)

type: integer

The maximum size (pixels) a component/cell can have (disabled by default)

type: integer

Enable the estimation of dynamic size filters using a log-rank approach both: estimate both min and max size, min: estimate min size (--min-size), max: estimate max size (--max-size)

type: string

Enable aggregate calling, information on potential aggregates will be added to the output data

type: boolean
default: true

Skip analysis step

type: boolean

Compute polarization scores matrix (clusters by markers)

type: boolean
default: true

Compute colocalization scores (marker by marker) for each component

type: boolean
default: true

Use the bipartite graph instead of the one-node projection when computing polarization, coabundance and colocalization scores

type: boolean

Which approach to use to normalize the antibody counts.

type: string
  • raw: use the raw counts.
  • CLR: use the CLR-transformed counts.
  • denoise: use CLR-transformed counts and subtract the counts of control antibodies

Transform the antibody counts to 0-1 (binarize) when computing polarization

type: boolean

Select the type of transformation to use on the node by antibody counts matrix when computing colocalization

type: string

Select the size of the neighborhood to use when computing colocalization metrics on each component

type: integer
default: 1

Set the number of permutations use to compute the empirical p-value for the colocalization score

type: integer
default: 50

The minimum number of counts in a region for it to be considered valid for computing colocalization

type: integer
default: 5

Skip report generation

type: boolean

Global configuration options specific to nf-core/pixelator.

Override the container image reference to use for all steps using the pixelator command.

type: string

Use this to force the pipeline to use a different image version in all steps that use the pixelator command.
The pipeline is not guaranteed to work when using different pixelator versions.

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|d|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

Display version and exit.

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

Incoming hook URL for messaging service

hidden
type: string

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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.

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warning.

Validation of parameters in lenient more.

hidden
type: boolean

Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.