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|yml|yaml)$

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})$

Save intermediate amplicon reads generated from the raw input reads.

type: boolean

Save intermediate amplicon reads generated from the raw input reads.

type: boolean

The number of mismatches allowed while anchoring reads using LBS sequences (in percentage of seen LBS length) [default: 0.1; 0.0<=x<=0.5]

type: number

Remove PolyG sequences (length of 10 or more)

type: boolean

Minimum average quality a read must have. Pass 0 to disable quality filtering.

type: integer
default: 20

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

The minimum length (bases) of a read

type: integer

The maximum number of Ns allowed in a read

type: integer

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

Save intermediate QC read files containing all reads that passed the filters.

type: boolean

Save intermediate QC read files containing all reads that failed the filters.

type: boolean

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

Save intermediate QC read files containing all reads that contain valid antibody barcodes.

type: boolean

Save intermediate QC read files containing all reads that failed the filters.

type: boolean

The number of mismatches allowed in marker barcodes.

type: number
default: 1

The target number of reads in a single file of the partitioned demux output.

type: string
default: 50M

The maximum number of chunks that the demuxed ouput for each umi region will be split into

type: number
default: 8

The demux and collapsing strategy to use

type: string

Save intermediate parquet files containing embeddings of all reads that contain valid antibody barcodes.

type: boolean

Save intermediate FASTQC read files containing all reads that contain valid antibody barcodes.

type: boolean

Save intermediate FASTQC read files containing all reads that do not contain valid antibody barcodes.

type: boolean

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

Save an intermediate parquet file containing collapsed read information.

type: boolean

The algorithm to use for collapsing.

type: string

The number of mismatches allowed when collapsing (adjacency)

type: integer
default: 2

Save an intermediate parquet file containing collapsed read information.

type: boolean

Activate the multiplet recovery using leiden community detection

type: boolean
default: true

The number of times a component can be broken down into smaller components during the multiplet recovery process.

hidden
type: integer
default: 5

Maximum number of edges between the produced components as a result of a component split operation during the multiplet recovery process.

hidden
type: integer
default: 5

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

hidden
type: integer
default: 2

Save an intermediate CSV file containing the unfiltered graph edge list.

type: boolean

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.

type: string

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

type: boolean
default: true

Save the raw_component_metrics.csv file from the annotate stage.

type: boolean

Save the PXL dataset after the annotate stage.

type: boolean

Save the PXL dataset after the graph stage.

type: boolean

Activate the multiplet recovery using leiden community detection

type: boolean
default: true

Number of iterations for the leiden algorithm.

type: number
default: 1

The resolution parameter for the leiden algorithm at the initial stage.

type: number
default: 1

The resolution parameter for the leiden algorithm at the refinement stage.

type: number
default: 0.01

Discard edges with a read count below given value. Set to 1 to disable filtering.

type: number
default: 1

The minimum component size to consider for refinement

type: number
default: 1000

The maximum recursion depth for the refinement algorithm. Set to 1 to disable refinement.

type: number
default: 5

The maximum number of edges to remove between components during the initial stage (iteration == 0) of multiplet recovery.

type: number

The maximum number of edges to remove between components during the refinement stage (iteration > 0) of multiplet recovery.

type: number
default: 4

The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the initial stage (iteration == 0) of multiplet recovery.

type: number

The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the refinement stage (iteration > 0) of multiplet recovery.

type: number

The minimum number of nodes in an potential new components in order for it to be pruned.

type: number
default: 100

Components with fewer nodes than this will be filtered from the output data. This is typically not needed. Setting this will disable the automatic size filtering.

type: number

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 transformation to use for the antibody counts when calculating polarity scores.

type: string

Set the number of permutations use to compute the empirical z- and p-values for the polarity score

type: integer
default: 50

The minimum number of counts of a marker to calculate the polarity score in the component

type: integer
default: 5

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

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

type: integer
default: 5

Save the PXL dataset after the analysis stage.

type: boolean

Save the PXL dataset after the analysis stage.

type: boolean

Compute proximity scores

type: boolean
default: true

Compute k-core summary tables for each component

type: boolean

Number of permutations to use when computing the expected proximity scores

type: integer
default: 100

Compute the variance explained by the SVD components

type: boolean
default: true

Number of pivots to use for the SVD decomposition

type: integer
default: 50

Skip layout step

type: boolean

Skip adding marker counts to the layout.

type: boolean

Select a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: fruchterman_reingold, fruchterman_reingold_3d, kamada_kawai, kamada_kawai_3d, pmds, pmds_3d, wpmds, wpmds_3d

type: string

Skip adding marker counts to the layout.

type: boolean

Select a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: pmds, pmds_3d, wpmds, wpmds_3d.

type: string

Number of pivots to use for the PMDS layout algorithm. Default: 50. More gives better results, but increases computation time.

type: integer
default: 50

The window size used when computing probability weights for the wpmds layout method. Only used when layout algorithm is set to wpmds.

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

Save all intermediate results.

type: boolean

Save all JSON report and metadata files generated by pixelator.

type: boolean
default: true

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/pixelator/

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