nf-core/scdownstream
A single cell transcriptomics pipeline for QC, integration and making the data presentable
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.
string
^\S+\.csv$
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.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email address for completion summary.
string
^([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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Options for mapping new data to a reference. Check the [section in the usage docs](https://nf-co.re/scdownstream/docs/usage/#reference-mapping) for more information.
If you want to project new data onto an already integrated object, specify the path to the base AnnData object here
string
^\S+\.h5ad$
The file should be in the .h5ad format.
The column in the base AnnData object that contains the label (e.g. cell type) information.
string
label
The keys in the obsm of the base AnnData object that contain the embeddings (without leading X_
). Required if input
is not provided - otherwise it is ignored.
string
^((scvi|scanvi|harmony|bbknn|combat|seurat)(,(scvi|scanvi|harmony|bbknn|combat|seurat))*)?$
If the input
parameter is not provided (no new data to add), integration will not be performed. In order to be able to utilize existing integration results, you need to provide the keys in the obsm of the base AnnData object that contain the embeddings (without leading X_
).
If you want to use a pre-trained scVI/scANVI model as a reference for integration, specify the path to the model .pt
file here
string
^\S+\.pt$
The file should be in the .pt format. If provided, you also need to provide a reference_model_type
.
Specify the type of model provided in the reference_model
parameter
string
scvi
Can be either 'scvi' or 'scanvi'.
This parameter must be a combination of the following values:scvi
, scanvi
Options for selecting which tools should be used for certain tasks
Only run the preprocessing steps, skip the integration and clustering steps
boolean
Scale the memory requirements for each process by this factor. Should be increased if you have a large number of cells.
integer
1
Specify the tool to use for ambient RNA removal
string
Specify the tools to use for doublet detection. Setting to 'none' will skip this step
string
scrublet
^(none|((solo|scrublet|doubletdetection|scds)?,?)*[^,]+$)
If you want to use multiple tools, separate them with a comma. Available methods are: solo, scrublet, doubletdetection, scds
Number of tools that need to agree on a doublet for it to be called as such
integer
1
Force keeping certain columns in the merged AnnData object, even if they are not present in all samples
string
^([a-zA-Z0-9_]*(,[a-zA-Z0-9_]*)*)?$
If you want to keep certain columns in the merged AnnData object, even if they are not present in all samples, specify them here. Separate them with a comma.
Specify the tool to use for integration
string
scvi
^((scvi|scanvi|harmony|bbknn|combat|seurat)(,(scvi|scanvi|harmony|bbknn|combat|seurat))*)?$
If you want to use multiple tools, separate them with a comma. Available methods are: scvi, scanvi, harmony, bbknn, combat, seurat
Number of highly variable genes to use for integration
integer
10000
Specify the resolutions for clustering
string
0.5,1.0
^((\d+\.?\d+)?,?)*[^,]+$
Specify the resolutions for clustering. If you want to use multiple resolutions, separate them with a comma.
Create a UMAP and a clustering for each unique value in the label column (and for each integration method)
boolean
Create a global UMAP and clustering (for each integration method)
boolean
true
Skip the rank_genes_groups step. For large datasets, the pipeline might fail due to high memory usage in this step. Use this option to skip it.
boolean
Specify the models to use for the celltypist cell type annotation
string
^([a-zA-Z0-9_]*(,[a-zA-Z0-9_]*)*)?$
If you want to use multiple models, separate them with a comma. Available models can be found here.
Number of epochs to train the CellBender model
integer
150
Method to aggregate gene expression values for non-unique genes
string
Method to aggregate gene expression values for non-unique genes. Available methods are: mean, sum, max
Use GPU acceleration for tasks that support it
boolean
Prepare the output for visualisation in cellxgene
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
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.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
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.
string
128.GB
^\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.
string
240.h
^(\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.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
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.
string
^([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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
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.
boolean
By default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
boolean
Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/