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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringReference genome related files and options required for the workflow.
Path to genome FASTA file.
string^\S+\.fn?a(sta)?(\.gz|\.zip)?$This parameter is mandatory if you wish to use isoquant as a quantifier
Path to transcriptome FASTA file.
string^\S+\.fn?a(sta)?(\.gz|\.zip)?$This parameter is mandatory if you wish to use oarfish as a quantifier
Path to GTF file.
string^\S+\.gtf(\.gz|\.zip)?$Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Do not load the iGenomes reference config.
booleantrueDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/This is the delimiter the FASTA uses in the sequence identifier to separate the string.
stringOptions related to processing fastqs
The number of lines to split the FASTQ into.
integerOptions to choose trimming criteria and software.
Choose minimum read length.
integer1Choose minimum average read quality score.
integer10Skip quality trimming step.
booleanOptions related to the barcode and umis.
User-provided file containing a list of cellular barcodes. Using this parameter will override the default whitelists provided by the pipeline and use the user-provided one instead.
stringSpecify the format for the barcode+umi. This parameter also defines a default barcode whitelist for the pipeline to use for barcode calling, this can be overridden with the 'whitelist' parameter.
stringSpecify which tool to be used for deduplication (Options: picard, umitools)
stringOptions related to minimap2.
Library strandness option.
stringMinimizer k-mer length.
integer14Save the secondary alignments when aligning to the genome
booleanSave the secondary alignments when aligning to the transcriptome
booleantrueOptions related to post-mapping analysis
Indicate whether to include introns in the count matrices
booleantrueProvide a comma-delimited options of quantifiers for the pipeline to use. Available tools: isoquant, oarfish
string^(oarfish|isoquant)(,(oarfish|isoquant))*$Options to skip various steps within the workflow.
Skip all QC.
booleanSkip FastQC.
booleanSkip Nanoplot.
booleanSkip ToulligQC.
booleanSkip NanoComp from FASTQ file(s).
booleanSkip NanoComp from BAM file(s).
booleanSkip RSeQC.
booleanSkip Seurat QC.
booleanSkip saving minimap2 index.
booleanSkip umi dedup.
booleanSkip MultiQC.
booleanParameters 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.
stringLess common options for the pipeline, typically set in a config file.
Display 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
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://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