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
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. 10x Genomics v2 Chemistry.
Can be ‘auto’ (cellranger only), ‘10XV1’, ‘10XV2’, ‘10XV3’, ‘10XV4’, or any other protocol string that will get directly passed the respective aligner.
stringautoThis section can be used to disable certain tools in the pipeline
Skip MultiQC Report
booleanSkip FastQC
booleanSkip cellbender empty drops filter subworkflow
booleanbooleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Do not load the iGenomes reference config.
booleanA cDNA FASTA file
stringReference GTF annotation file
stringSpecify this parameter to save the indices created (STAR, Kallisto, Simpleaf) to the results.
booleanSpecify this parameter to save the intermediate alignment files (STAR, CellRanger) to the results.
booleanDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Path to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Kallisto/BUS and Alevin-fry with AlevinQC.
stringPath to pre-built Simpleaf index.
stringUMI resolution strategy to deduplicate UMIs.
stringSpecify 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 path to the precomputed Kallisto index.
stringSpecify a path to the cDNA transcripts-to-capture.
stringSpecify a path to the intron transcripts-to-capture.
stringType of workflow. Use nac for an index type that can quantify nascent and mature RNA. Use lamanno for RNA velocity based on La Manno et al. 2018 logic. (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. Provide the base directory of the index (e.g., ‘/PATH/TO/10X_REF/refdata-gex-GRCh38-2024-A/’)
stringShould it skip the automatic renaming included in cellranger-related modules?
booleanParams related to the Cellranger pipeline
Specify a motif file to create a cellranger-arc index. Can be taken, e.g., from the JASPAR database.
stringSpecify a config file to create the cellranger-arc index.
stringSpecify the genome reference name used in the config file to create a cellranger-arc index.
stringSpecify a pre-built Cell Ranger index for VDJ analysis.
stringSkip mkvdjref if not using VDJ data with cellranger/multi
booleanProvide a probe set for fixed RNA-seq profiling (used with FFPE samples). Please refer to the 10x documentation about probesets for more details.
stringProvide a panel description for targeted sequencing.
stringProvide a Cell Multiplexing Oligo (CMO) description file when working with multiplexed samples. This is only necessary if you with to override Cell Ranger’s default CMO-set. Please refer to the 10x documentation about CMO references for more details.
stringProvide a reference file for feature barcoding (e.g. antibody measurements). Please refer to the Cell Ranger Feature Reference documentation for more details.
stringThis argument takes a .txt file containing primer sequences that were used to enrich cDNA for V(D)J sequences. This is only necessary if you with to override Cell Ranger’s defaults.
stringThis is only necessary to override Cell Ranger’s default cell calling and tag calling steps. In most cases, you need to only use the cellranger_multi_barcodes parameter. Please refer to the 10x documentation for more information about this file.
stringAdditional samplesheet to provide information about multiplexed samples. See the ‘Usage’ section for more details.
stringParameters 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.
stringLess common options for the pipeline, typically set in a config file.
Display 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.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string