nf-core/scnanoseq
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
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
Reference genome related files and options required for the workflow.
Path to genome FASTA file.
string
^\S+\.fn?a(sta)?(\.gz|\.zip)?$
Path to transcriptome FASTA file.
string
^\S+\.fn?a(sta)?(\.gz|\.zip)?$
Path to GTF file.
string
^\S+\.gtf(\.gz|\.zip)?$
Name of iGenomes reference.
string
Do not load the iGenomes reference config.
boolean
true
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
This is the delimiter the FASTA uses in the sequence identifier to separate the string.
string
Options related to processing fastqs
The number of lines to split the FASTQ into.
integer
Options to choose trimming criteria and software.
Choose minimum read length.
integer
1
Choose minimum average read quality score.
integer
10
Skip quality trimming step.
boolean
Options related to the barcode and umis.
User-provided file containing a list of cellular barcodes. Using this parameter will override the default whitelists provided by the pipeline and use the user-provided one instead.
string
Specify the format for the barcode+umi. This parameter also defines a default barcode whitelist for the pipeline to use for barcode calling, this can be overridden with the ‘whitelist’ parameter.
string
Specify which tool to be used for deduplication (Options: picard, umitools)
string
Options related to minimap2.
Library strandness option.
string
Minimizer k-mer length.
integer
14
Save the secondary alignments when aligning to the genome
boolean
Save the secondary alignments when aligning to the transcriptome
boolean
true
Options related to post-mapping analysis
Indicate whether to include introns in the count matrices
boolean
true
Provide a comma-delimited options of quantifiers for the pipeline to use. Available tools: isoquant, oarfish
string
Options to skip various steps within the workflow.
Skip all QC.
boolean
Skip FastQC.
boolean
Skip Nanoplot.
boolean
Skip ToulligQC.
boolean
Skip NanoComp from FASTQ file(s).
boolean
Skip NanoComp from BAM file(s).
boolean
Skip RSeQC.
boolean
Skip Seurat QC.
boolean
Skip saving minimap2 index.
boolean
Skip umi dedup.
boolean
Skip MultiQC.
boolean
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
Less common options for the pipeline, typically set in a config file.
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
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://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