nf-core/alleleexpression
Alleleexpression is a nf-core pipeline for allele-specific expression (ASE) analysis using STAR-WASP for alignment, UMI-tools for deduplication, and phaser for haplotype phasing and ASE detection.
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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
MultiQC report title. Written as page header in MultiQC report.
stringReference genome related files and options required for the workflow.
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.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to GTF annotation file.
string^\S+\.gtf(\.gz)?$Path to directory containing STAR genome index.
stringPath to BED file with gene features for phaser_gene_ae.
string^\S+\.bed(\.gz)?$Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanOptions for chromosome selection and variant phasing.
Chromosome to analyze for ASE.
stringnullPath to Beagle reference panel VCF file.
string^\S+\.vcf(\.gz)?$Path to Beagle genetic map file.
stringOptions for UMI processing.
UMI separator character in read IDs.
string: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 config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringInstitutional config name.
stringLess common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay 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})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$If 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.
Incoming 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 be the same when using MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBy default, parameters defined in the schema are automatically validated. Disable this to avoid errors if you have any parameters that are not defined in the schema.
Show all params when using --help
booleanComma-separated list of params names to ignore during schema validation
stringgenomes,modulesInternal parameter to store module-specific options.
string