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
1.1.0
). The latest
stable release is
4.0.0
.
Define where the pipeline should find input data and save output data.
Input FastQ files
string
Input FastQ files path in array format
string
The output directory where the results will be saved.
string
./results
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Name of droplet technology (Currently supported: 10x, Drop-Seq, inDrop, etc may be supported in the future.)
string
10x
Version of 10x chemistry
string
V3
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. Available are: “alevin”, “star”, “kallisto”. Default ‘alevin’.
string
alevin
Options for the reference genome indices used to align reads.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes/
Do not load the iGenomes reference config.
boolean
A cDNA fastq file
string
Reference GTF annotation file
string
Specify this parameter to save the indices created (STAR, Kallisto, Salmon) to the results.
string
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
Specify a path to the precomputed STAR index.
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
If set to false, skip the correct steps after mapping with Kallisto.
boolean
Skip BUStools entirely in workflow
boolean
Specify a path to the precomputed Kallisto index.
string
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Method used to save pipeline results to output directory.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
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
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Show all params when using --help
boolean
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^[\d\.]+\s*.(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^[\d\.]+\.*(s|m|h|d)$
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 configs hostname.
string
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string