nf-core/scrnaseq
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
2.3.2). The latest
stable release is
4.0.0
.
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringIf not using the 10X Genomics platform, a custom barcode whitelist can be used with --barcode_whitelist.
stringName of the tool to use for scRNA (pseudo-) alignment.
stringThe protocol that was used to generate the single cell data, e.g. 10XV2 (default).
stringThis section can be used to disable certain tools in the pipeline
Skip MultiQC Report
booleanSkip FastQC
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanA cDNA FASTA file
stringReference GTF annotation file
stringSpecify this parameter to save the indices created (STAR, Kallisto, Salmon) to the results.
booleanThis can be used to specify a precomputed Salmon index in the pipeline, in order to skip the generation of required indices by Salmon itself.
stringPath to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.
stringIt is the target read length the index will be built for, using simpleaf.
integer91Specify a path to the precomputed STAR index.
stringIgnore the SJDB GTF file.
stringName of sequencing center for BAM read group tag.
stringQuantification type of different transcriptomic feature. Use GeneFull on pre-mRNA count for single-nucleus RNA-seq reads. Use Gene Velocyto to generate RNA velocity matrix.
stringParams related to Kallisto/BUS tool
Specify a Kallisto gene mapping file here. If you don’t, this will be automatically created in the Kallisto workflow when specifying a valid --gtf file.
stringSpecify a path to the precomputed Kallisto index.
stringType of workflow. Use lamanno for RNA velocity based on La Manno et al. 2018 logic. Use nucleus for RNA velocity on single-nucleus RNA-seq reads. Use kite for feature barcoding. Use kite: 10xFB for 10x Genomics Feature Barcoding technology. (default: standard)
stringParams related to the Cellranger pipeline
Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website.
stringParams related to the Cellranger pipeline
Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website.
stringSpecify a single-cell technology, vendor, or platform. See the UniverSC documentation or GitHub repository for more details.
string10xParameters 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 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.
string128.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*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
boolean