nf-core/scflow
Please consider using/contributing to https://github.com/nf-core/scdownstream
Define where the pipeline should find input data and save output data.
The .tsv file specifying sample matrix filepaths.
string./refs/Manifest.txtThe .tsv file specifying sample metadata.
string./refs/SampleSheet.tsvOptional tsv file containing mappings between ensembl_gene_id’s and gene_names’s
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/scflow/assets/ensembl_mappings.tsvCell-type annotations reference file path
stringhttps://s3-eu-west-1.amazonaws.com/pfigshare-u-files/28033407/ctd_v1.zipOptional tsv file specifying manual revisions of cell-type annotations.
string./conf/celltype_mappings.tsvOptional list of genes of interest in YML format for plotting of gene expression.
string./conf/reddim_genes.ymlInput sample species.
stringhumanOutputs directory.
string./resultsParameters for quality-control and thresholding.
The sample sheet column name with unique sample identifiers.
stringmanifestThe sample sheet variables to treat as factors.
stringseqdateMinimum library size (counts) per cell.
integer250Maximum library size (counts) per cell.
stringadaptiveMinimum features (expressive genes) per cell.
integer100Maximum features (expressive genes) per cell.
stringadaptiveMinimum proportion of counts mapping to ribosomal genes.
numberMaximum proportion of counts mapping to ribosomal genes.
number1Maximum proportion of counts mapping to mitochondrial genes.
stringadaptiveMinimum counts for gene expressivity.
integer2Minimum cells for gene expressivity.
integer2Option to drop unmapped genes.
stringTrueOption to drop mitochondrial genes.
stringTrueOption to drop ribosomal genes.
stringfalseThe number of MADs for outlier detection.
number4Options for profiling ambient RNA/empty droplets.
Enable ambient RNA / empty droplet profiling.
stringtrueUpper UMI counts threshold for true cell annotation.
stringautoLower UMI counts threshold for empty droplet annotation.
integer100The maximum FDR for the emptyDrops algorithm.
number0.001Number of Monte Carlo p-value iterations.
integer10000Expected number of cells per sample.
integer3000Parameters for identifying singlets/doublets/multiplets.
Enable doublet/multiplet identification.
stringtrueAlgorithm to use for doublet/multiplet identification.
stringdoubletfinderVariables to regress out for dimensionality reduction.
stringnCount_RNA,pc_mitoNumber of PCA dimensions to use.
integer10The top n most variable features to use.
integer2000A fixed doublet rate.
numberDoublets per thousand cells increment.
integer8Specify a pK value instead of parameter sweep.
number0.02Parameters used in the merged quality-control report.
Numeric variables for inter-sample metrics.
stringtotal_features_by_counts,total_counts,pc_mito,pc_riboCategorical variables for further sub-setting of plots
stringNULLNumeric variables for outlier identification.
stringtotal_features_by_counts,total_countsParameters for integrating datasets and batch correction.
Choice of integration method.
stringLigerUnique sample identifier variable.
stringmanifestFill out matrices with union of genes.
stringfalseRemove non-expressing cells/genes.
stringtrueNumber of genes to find for each dataset.
integer3000How to combine variable genes across experiments.
stringunionKeep unique genes.
stringfalseCapitalize gene names to match homologous genes.
stringfalseTreat each column as a cell.
stringtrueInner dimension of factorization (n factors).
integer30Regularization parameter.
number5Convergence threshold.
number0.0001Maximum number of block coordinate descent iterations.
integer100Number of restarts to perform.
integer1Random seed for reproducible results.
integer1Number of neearest neighbours for within-dataset knn graph.
integer20Horizon parameter for shared nearest factor graph.
integer500Minimum allowed edge weight.
number0.2Name of dataset to use as a reference.
stringNULLMinimum number of cells to consider a cluster shared across datasets.
integer2Number of quantiles to use for normalization.
integer50Number of times to perform Louvain community detection.
integer10Controls the number of communities detected.
integer1Indices of factors to use for shared nearest factor determination.
stringNULLDistance metric to use in calculating nearest neighbour.
stringCRCenter the data when scaling factors.
stringfalseSmall cluster extraction cells threshold.
integerCategorical variables for integration report metrics.
stringindividual,diagnosis,region,sexReduced dimension embedding for the integration report.
stringUMAPSettings for dimensionality reduction algorithms.
Input matrix for dimension reduction.
stringPCA,LigerDimension reduction outputs to generate.
stringtSNE,UMAP,UMAP3DVariables to regress out before dimension reduction.
stringnCount_RNA,pc_mitoNumber of PCA dimensions.
integer30Number of nearest neighbours to use.
integer35The dimension of the space to embed into.
integer2Type of initialization for the coordinates.
stringDistance metric for finding nearest neighbours.
stringNumber of epochs to us during optimization of embedded coordinates.
integer200Initial learning rate used in optimization of coordinates.
integer1Effective minimum distance between embedded points.
number0.4Effective scale of embedded points.
number0.85Interpolation to combine local fuzzy sets.
number1Local connectivity required.
integer1Weighting applied to negative samples in embedding optimization.
integer1Number of negative edge samples to use per positive edge sample.
integer5Use fast SGD.
stringfalseOutput dimensionality.
integer2Number of dimensions retained in the initial PCA step.
integer50Perplexity parameter.
integer150Speed/accuracy trade-off.
number0.5Iteration after which perplexities are no longer exaggerated.
integer250Iteration after which the final momentum is used.
integer250Number of iterations.
integer1000Center data before PCA.
stringtrueScale data before PCA.
stringfalseNormalize data before distance calculations.
stringtrueMomentum used in the first part of optimization.
number0.5Momentum used in the final part of optimization.
number0.8Learning rate.
integer1000Exaggeration factor used in the first part of the optimization.
integer12Parameters used to tune louvain/leiden clustering.
Clustering method.
stringleidenReduced dimension input(s) for clustering.
stringUMAP_LigerThe resolution of clustering.
number0.001Integer number of nearest neighbours for clustering.
integer50The number of iterations for clustering.
integer1Parameters used for cell-type annotation and the associated report.
SingleCellExperiment clusters colData variable name.
stringclustersMax cells to sample.
integer10000A sample metadata unique sample ID.
stringindividualSingleCellExperiment cell-type colData variable name.
stringcluster_celltypeCell-type metrics for categorical variables.
stringmanifest,diagnosis,sex,capdate,prepdate,seqdateCell-type metrics for numeric variables.
stringpc_mito,pc_ribo,total_counts,total_features_by_countsNumber of top marker genes for plot/table generation.
integer5Parameters for differential gene expression.
Differential gene expression method.
stringMASTZLMMAST method.
stringExpressive gene minimum counts.
integer1Expressive gene minimum cells fraction.
number0.1Re-scale numeric covariates.
stringtruePseudobulked differential gene expression.
stringfalseCell-type annotation variable name.
stringcluster_celltypeUnique sample identifier variable.
stringmanifestDependent variable of DGE model.
stringgroupReference class of categorical dependent variable.
stringControlConfounding variables.
stringcngeneson,seqdate,pc_mitoRandom effect confounding variable.
stringNULLFold-change threshold for plotting.
number1.1Adjusted p-value cutoff.
number0.05Force model fit for non-full rank.
stringfalseMaximum CPU cores.
string'null'Parameters for impacted pathway analysis of differentially expressed genes.
Pathway enrichment tool(s) to use.
stringEnrichment method.
stringORADatabase(s) to use for enrichment.
stringGO_Biological_ProcessParameters for dirichlet modeling of relative cell-type proportions.
Unique sampler identifier.
stringindividualCell-type annotation variable name.
stringcluster_celltypeDependent variable of Dirichlet model.
stringgroupReference class of categorical dependent variable.
stringControlDependent variable classes order.
stringControl,Low,HighGeneral parameters for plotting.
Preferred embedding for plots.
stringUMAP_LigerPoint size for reduced dimension plots.
number0.1Alpha (transparency) value for reduced dimension plots.
number0.2Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string256.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Do not use coloured log outputs.
booleanDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
booleanInstead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
booleanE-mail address for optional workflow completion notification.
stringSend plain-text email instead of HTML.
booleanNA
string