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

The .tsv file specifying sample matrix filepaths.

required
type: string
default: ./refs/Manifest.txt

The .tsv file specifying sample metadata.

required
type: string
default: ./refs/SampleSheet.tsv

Optional tsv file containing mappings between ensembl_gene_id’s and gene_names’s

required
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/scflow/assets/ensembl_mappings.tsv

Cell-type annotations reference file path

required
type: string
default: https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/28033407/ctd_v1.zip

Optional tsv file specifying manual revisions of cell-type annotations.

type: string
default: ./conf/celltype_mappings.tsv

Optional list of genes of interest in YML format for plotting of gene expression.

type: string
default: ./conf/reddim_genes.yml

Input sample species.

required
type: string
default: human

Outputs directory.

type: string
default: ./results

Parameters for quality-control and thresholding.

The sample sheet column name with unique sample identifiers.

required
type: string
default: manifest

The sample sheet variables to treat as factors.

required
type: string
default: seqdate

Minimum library size (counts) per cell.

required
type: integer
default: 250

Maximum library size (counts) per cell.

required
type: string
default: adaptive

Minimum features (expressive genes) per cell.

required
type: integer
default: 100

Maximum features (expressive genes) per cell.

required
type: string
default: adaptive

Minimum proportion of counts mapping to ribosomal genes.

type: number

Maximum proportion of counts mapping to ribosomal genes.

required
type: number
default: 1

Maximum proportion of counts mapping to mitochondrial genes.

required
type: string
default: adaptive

Minimum counts for gene expressivity.

required
type: integer
default: 2

Minimum cells for gene expressivity.

required
type: integer
default: 2

Option to drop unmapped genes.

required
type: string
default: True

Option to drop mitochondrial genes.

required
type: string
default: True

Option to drop ribosomal genes.

required
type: string
default: false

The number of MADs for outlier detection.

required
type: number
default: 4

Options for profiling ambient RNA/empty droplets.

Enable ambient RNA / empty droplet profiling.

required
type: string
default: true

Upper UMI counts threshold for true cell annotation.

required
type: string
default: auto

Lower UMI counts threshold for empty droplet annotation.

required
type: integer
default: 100

The maximum FDR for the emptyDrops algorithm.

required
type: number
default: 0.001

Number of Monte Carlo p-value iterations.

required
type: integer
default: 10000

Expected number of cells per sample.

required
type: integer
default: 3000

Parameters for identifying singlets/doublets/multiplets.

Enable doublet/multiplet identification.

required
type: string
default: true

Algorithm to use for doublet/multiplet identification.

required
type: string
default: doubletfinder

Variables to regress out for dimensionality reduction.

required
type: string
default: nCount_RNA,pc_mito

Number of PCA dimensions to use.

required
type: integer
default: 10

The top n most variable features to use.

required
type: integer
default: 2000

A fixed doublet rate.

type: number

Doublets per thousand cells increment.

required
type: integer
default: 8

Specify a pK value instead of parameter sweep.

required
type: number
default: 0.02

Parameters used in the merged quality-control report.

Numeric variables for inter-sample metrics.

required
type: string
default: total_features_by_counts,total_counts,pc_mito,pc_ribo

Categorical variables for further sub-setting of plots

required
type: string
default: NULL

Numeric variables for outlier identification.

required
type: string
default: total_features_by_counts,total_counts

Parameters for integrating datasets and batch correction.

Choice of integration method.

required
type: string
default: Liger

Unique sample identifier variable.

required
type: string
default: manifest

Fill out matrices with union of genes.

required
type: string
default: false

Remove non-expressing cells/genes.

required
type: string
default: true

Number of genes to find for each dataset.

required
type: integer
default: 3000

How to combine variable genes across experiments.

required
type: string
default: union

Keep unique genes.

required
type: string
default: false

Capitalize gene names to match homologous genes.

required
type: string
default: false

Treat each column as a cell.

required
type: string
default: true

Inner dimension of factorization (n factors).

required
type: integer
default: 30

Regularization parameter.

required
type: number
default: 5

Convergence threshold.

required
type: number
default: 0.0001

Maximum number of block coordinate descent iterations.

required
type: integer
default: 100

Number of restarts to perform.

required
type: integer
default: 1

Random seed for reproducible results.

required
type: integer
default: 1

Number of neearest neighbours for within-dataset knn graph.

required
type: integer
default: 20

Horizon parameter for shared nearest factor graph.

required
type: integer
default: 500

Minimum allowed edge weight.

required
type: number
default: 0.2

Name of dataset to use as a reference.

required
type: string
default: NULL

Minimum number of cells to consider a cluster shared across datasets.

required
type: integer
default: 2

Number of quantiles to use for normalization.

required
type: integer
default: 50

Number of times to perform Louvain community detection.

required
type: integer
default: 10

Controls the number of communities detected.

required
type: integer
default: 1

Indices of factors to use for shared nearest factor determination.

required
type: string
default: NULL

Distance metric to use in calculating nearest neighbour.

required
type: string
default: CR

Center the data when scaling factors.

required
type: string
default: false

Small cluster extraction cells threshold.

type: integer

Categorical variables for integration report metrics.

required
type: string
default: individual,diagnosis,region,sex

Reduced dimension embedding for the integration report.

required
type: string
default: UMAP

Settings for dimensionality reduction algorithms.

Input matrix for dimension reduction.

required
type: string
default: PCA,Liger

Dimension reduction outputs to generate.

required
type: string
default: tSNE,UMAP,UMAP3D

Variables to regress out before dimension reduction.

required
type: string
default: nCount_RNA,pc_mito

Number of PCA dimensions.

required
type: integer
default: 30

Number of nearest neighbours to use.

required
type: integer
default: 35

The dimension of the space to embed into.

required
type: integer
default: 2

Type of initialization for the coordinates.

required
type: string

Distance metric for finding nearest neighbours.

required
type: string

Number of epochs to us during optimization of embedded coordinates.

required
type: integer
default: 200

Initial learning rate used in optimization of coordinates.

required
type: integer
default: 1

Effective minimum distance between embedded points.

required
type: number
default: 0.4

Effective scale of embedded points.

required
type: number
default: 0.85

Interpolation to combine local fuzzy sets.

required
type: number
default: 1

Local connectivity required.

required
type: integer
default: 1

Weighting applied to negative samples in embedding optimization.

required
type: integer
default: 1

Number of negative edge samples to use per positive edge sample.

required
type: integer
default: 5

Use fast SGD.

required
type: string
default: false

Output dimensionality.

required
type: integer
default: 2

Number of dimensions retained in the initial PCA step.

required
type: integer
default: 50

Perplexity parameter.

required
type: integer
default: 150

Speed/accuracy trade-off.

required
type: number
default: 0.5

Iteration after which perplexities are no longer exaggerated.

required
type: integer
default: 250

Iteration after which the final momentum is used.

required
type: integer
default: 250

Number of iterations.

required
type: integer
default: 1000

Center data before PCA.

required
type: string
default: true

Scale data before PCA.

required
type: string
default: false

Normalize data before distance calculations.

required
type: string
default: true

Momentum used in the first part of optimization.

required
type: number
default: 0.5

Momentum used in the final part of optimization.

required
type: number
default: 0.8

Learning rate.

required
type: integer
default: 1000

Exaggeration factor used in the first part of the optimization.

required
type: integer
default: 12

Parameters used to tune louvain/leiden clustering.

Clustering method.

required
type: string
default: leiden

Reduced dimension input(s) for clustering.

required
type: string
default: UMAP_Liger

The resolution of clustering.

required
type: number
default: 0.001

Integer number of nearest neighbours for clustering.

required
type: integer
default: 50

The number of iterations for clustering.

required
type: integer
default: 1

Parameters used for cell-type annotation and the associated report.

SingleCellExperiment clusters colData variable name.

required
type: string
default: clusters

Max cells to sample.

required
type: integer
default: 10000

A sample metadata unique sample ID.

required
type: string
default: individual

SingleCellExperiment cell-type colData variable name.

required
type: string
default: cluster_celltype

Cell-type metrics for categorical variables.

required
type: string
default: manifest,diagnosis,sex,capdate,prepdate,seqdate

Cell-type metrics for numeric variables.

required
type: string
default: pc_mito,pc_ribo,total_counts,total_features_by_counts

Number of top marker genes for plot/table generation.

required
type: integer
default: 5

Parameters for differential gene expression.

Differential gene expression method.

required
type: string
default: MASTZLM

MAST method.

required
type: string

Expressive gene minimum counts.

required
type: integer
default: 1

Expressive gene minimum cells fraction.

required
type: number
default: 0.1

Re-scale numeric covariates.

required
type: string
default: true

Pseudobulked differential gene expression.

required
type: string
default: false

Cell-type annotation variable name.

required
type: string
default: cluster_celltype

Unique sample identifier variable.

required
type: string
default: manifest

Dependent variable of DGE model.

required
type: string
default: group

Reference class of categorical dependent variable.

required
type: string
default: Control

Confounding variables.

required
type: string
default: cngeneson,seqdate,pc_mito

Random effect confounding variable.

required
type: string
default: NULL

Fold-change threshold for plotting.

required
type: number
default: 1.1

Adjusted p-value cutoff.

required
type: number
default: 0.05

Force model fit for non-full rank.

required
type: string
default: false

Maximum CPU cores.

required
type: string
default: 'null'

Parameters for impacted pathway analysis of differentially expressed genes.

Pathway enrichment tool(s) to use.

required
type: string

Enrichment method.

required
type: string
default: ORA

Database(s) to use for enrichment.

required
type: string
default: GO_Biological_Process

Parameters for dirichlet modeling of relative cell-type proportions.

Unique sampler identifier.

required
type: string
default: individual

Cell-type annotation variable name.

required
type: string
default: cluster_celltype

Dependent variable of Dirichlet model.

required
type: string
default: group

Reference class of categorical dependent variable.

required
type: string
default: Control

Dependent variable classes order.

required
type: string
default: Control,Low,High

General parameters for plotting.

Preferred embedding for plots.

required
type: string
default: UMAP_Liger

Point size for reduced dimension plots.

required
type: number
default: 0.1

Alpha (transparency) value for reduced dimension plots.

required
type: number
default: 0.2

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 configs hostname.

hidden
type: string

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: 256.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})$

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

Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.

hidden
type: boolean

E-mail address for optional workflow completion notification.

hidden
type: string

Send plain-text email instead of HTML.

hidden
type: boolean

NA

hidden
type: string