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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Written as page header in MultiQC report.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file. Required when --star_index is not given.
string^\S+\.fn?a(sta)?(\.gz)?$Path to GTF annotation file.
string^\S+\.gtf(\.gz)?$Path to directory containing a pre-built STAR index. If not given, it is built from --fasta and --gtf.
stringSave the STAR index built by the pipeline to <outdir>/genome/index so it can be reused with --star_index.
booleanPath to BED file with gene features for phaser_gene_ae.
string^\S+\.bed(\.gz)?$Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanOptions for chromosome selection and variant phasing.
Chromosome to analyze for ASE.
stringchr11Path to Beagle reference panel VCF file.
string^\S+\.vcf(\.gz)?$Path to Beagle genetic map file.
stringOptions for UMI processing.
UMI separator character in read IDs.
string:Options for calling allele-specific expression from gene-level haplotype counts.
Statistical test for allele-specific expression: binomial or betabinomial.
stringMinimum haplotypic reads (aCount + bCount) for a gene to be tested for ASE.
integer20Benjamini-Hochberg FDR threshold for calling a gene ASE.
number0.05Minimum effect size to call a gene ASE, as |major haplotype fraction - 0.5|.
numberFixed beta-binomial overdispersion (rho) for --ase_test betabinomial. Estimated from the data if not set.
numberFraction of tested genes left out when estimating the beta-binomial overdispersion.
number0.2Parameters 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.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom 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
booleantrueShow 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