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
stringUse this to specify the location of your input FastQ files. For example:
--input 'path/to/data/sample_*_{1,2}.fastq'
Please note the following requirements:
- The path must be enclosed in quotes
- The path must have at least one
*wildcard character - When using the pipeline with paired end data, the path must use
{1,2}notation to specify read pairs.
If left unspecified, a default pattern is used: data/*{1,2}.fastq.gz
Input 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})$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.
Name of droplet technology (Currently supported: 10x, Drop-Seq, inDrop, etc may be supported in the future.)
string10xVersion of 10x chemistry
stringV3To specify which chemistry (and thus barcode whitelist) to use, use the --chemistry flag. For example, to specify V3 chemistry (the default, as it is compatible with V2), use --chemistry V3.
These files were copied out of 10x Genomics' cellranger cellranger/lib/python/cellranger/barcodes, in some cases gzipped for simplicity across versions, and copied to assets/whitelist.
- V1:
737K-april-2014_rc.txt--> gzipped -->10x_V1_barcode_whitelist.txt.gz - V2:
737K-august-2016.txt--> gzipped -->10x_V2_barcode_whitelist.txt.gz - V3:
3M-february-2018.txt.gz-->10x_V3_barcode_whitelist.txt.gz
If 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'.
stringalevinThe workflow can handle three types of methods:
- Kallisto/Bustools
- Salmon Alevin + AlevinQC
- STARsolo
To choose which one to use, please specify either alevin, star or kallisto as a parameter option for --aligner. By default, the pipeline runs the alevin option. Note that specifying another aligner option also requires choosing appropriate parameters (see below) for the selected option.
Options for the reference genome indices used to align reads.
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.
Path to FASTA genome file.
stringIf you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanDo 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.
A 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.
stringThis is not the same as the
kallisto_gene_mapparameter down below and is only used by the Salmon Alevin workflow.
Specify a path to the precomputed STAR index.
stringNB: This has to be computed with STAR Version 2.7 or later, as STARsolo was only first supported by STAR Version 2.7.
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.
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.
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.
Boolean 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})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MBIf file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Custom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^[\d\.]+\s*.(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^[\d\.]+\.*(s|m|h|d)$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base 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 the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string