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
stringInput FastQ files path in array format
stringThe output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Name of droplet technology (Currently supported: 10x, Drop-Seq, inDrop, etc may be supported in the future.)
string10xVersion of 10x chemistry
stringV3If not using the 10X Genomics platform, a custom barcode whitelist can be used with --barcode_whitelist.
stringName of the tool to use for scRNA (pseudo-) alignment. Available are: “alevin”, “star”, “kallisto”. Default ‘alevin’.
stringalevinOptions for the reference genome indices used to align reads.
Name of iGenomes reference.
stringPath to FASTA genome file.
stringDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanA cDNA fastq file
stringReference GTF annotation file
stringSpecify this parameter to save the indices created (STAR, Kallisto, Salmon) to the results.
stringThis can be used to specify a precomputed Salmon index in the pipeline, in order to skip the generation of required indices by Salmon itself.
stringPath to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.
stringSpecify a path to the precomputed STAR index.
stringParams related to Kallisto/BUS tool
Specify a Kallisto gene mapping file here. If you don’t, this will be automatically created in the Kallisto workflow when specifying a valid --gtf file.
stringIf set to false, skip the correct steps after mapping with Kallisto.
booleanSkip BUStools entirely in workflow
booleanSpecify a path to the precomputed Kallisto index.
stringLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^[\d\.]+\s*.(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^[\d\.]+\.*(s|m|h|d)$Parameters 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/masterInstitutional configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string