nf-core/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
2.4.0
). The latest
stable release is
3.0.0
.
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.
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
If not using the 10X Genomics platform, a custom barcode whitelist can be used with --barcode_whitelist
.
string
Name of the tool to use for scRNA (pseudo-) alignment.
string
The 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. 10XV2 (default).
string
This section can be used to disable certain tools in the pipeline
Skip MultiQC Report
boolean
Skip FastQC
boolean
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
If 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.
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Do 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
string
Reference GTF annotation file
string
Specify this parameter to save the indices created (STAR, Kallisto, Salmon) to the results.
boolean
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.
string
Path to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.
string
This is not the same as the
kallisto_gene_map
parameter down below and is only used by the Salmon Alevin workflow.
It is the target read length the index will be built for, using simpleaf.
integer
91
Specify a path to the precomputed STAR index.
string
NB: 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.
string
Name of sequencing center for BAM read group tag.
string
Quantification 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.
string
Params 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.
string
Specify a path to the precomputed Kallisto index.
string
Type 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)
string
Params related to the Cellranger pipeline
Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website.
string
Params related to the Cellranger pipeline
Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website.
string
Specify a single-cell technology, vendor, or platform. See the UniverSC documentation or GitHub repository for more details.
string
10x
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.