nf-core/spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
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$You will need to create a design file with information about the samples in your experiment before running the pipeline, use this parameter to specify its location. It has to be a comma-separated file with 2 or 5 columns, plus a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringOptions related to Space Ranger execution and raw spatial data processing
Location of Space Ranger probeset file.
string^\S+\.csv$Location of Space Ranger reference directory. May be packed as tar.gz file.
stringhttps://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gzPlease see the 10x website to download either of the supported human or mouse references. If not specified the GRCh38 human reference is automatically downladed and used.
Additional intermediate output files that can be optionally saved.
Save the extracted tar archive of the Space Ranger reference.
booleanBy default, extracted versions of archived Space Ranger reference data will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.
Save extracted tar archives of input data.
booleanBy default, extracted versions of archived input data will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.
Options related to the downstream analyses performed by the pipeline.
The minimum number of UMIs needed in a spot for that spot to pass the filtering.
integer500The minimum number of expressed genes in a spot needed for that spot to pass the filtering.
integer250The minimum number of spots in which a gene is expressed for that gene to pass the filtering.
integer1The maximum proportion of mitochondrial content that a spot is allowed to have to pass the filtering.
number20If you do not wish to filter based on mitochondrial content, set this parameter to 100.
The minimum proportion of ribosomal content that a spot is needs to have to pass the filtering (no filtering is done by default).
numberThe maximum proportion of haemoglobin content that a spot is allowed to have to pass the filtering (no filtering is done by default).
number100The number of top highly variable genes to use for the analyses.
integer2000The resolution for the clustering of the spots.
number1The resolution controls the coarseness of the clustering, where a higher resolution leads to more clusters.
The method to use for spatially variable gene autocorrelation.
stringThe number of top spatially variable genes to plot.
integer14Parameters 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/masterIf 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.
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.
integer64Use 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.
string128.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.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy 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.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.