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
2.7.1). 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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
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 workflow can handle three types of methods:
- Kallisto/Bustools
- Salmon Alevin + AlevinQC
- STARsolo
To choose which one to use, please specify either alevin, star or kallisto as a parameter option for --aligner. By default, the pipeline runs the alevin option. Note that specifying another aligner option also requires choosing appropriate parameters (see below) for the selected option.
The 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.
stringautoThe default is to auto-detect the protocol when running cellranger. For all other aligners the protocol MUST be manually specified.
The following protocols are recognized by the pipeline and mapped to the corresponding protocol name of the respective aligner: '10XV1', '10XV2', '10XV3', '10XV4'.
Any other protocol value is passed to the aligner in verbatim to support other sequencing platforms. See the kallisto, simpleaf, starsolo, and universc documentations for more details.
This section can be used to disable certain tools in the pipeline
Skip MultiQC Report
booleanSkip FastQC
booleanSkip custom empty drops filter module
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
A cDNA FASTA file
stringReference GTF annotation file
stringSpecify this parameter to save the indices created (STAR, Kallisto, Salmon) to the results.
booleanDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/This 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.
stringThis is only used by the Salmon Alevin workflow.
It is the target read length the index will be built for, using simpleaf.
integer91Specify a path to the precomputed STAR index.
stringNB: This has to be computed with STAR Version 2.7 or later, as STARsolo was only first supported by STAR Version 2.7.
Ignore 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)
stringActivate Kallisto/BUStools filtering algorithm
booleanParams related to the Cellranger pipeline
Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website.
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.
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 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/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.
integer16Use 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.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/