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.
string
Email 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.
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 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
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
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
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
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
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
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
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
Email 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.
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
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
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean