nf-core/abotyper
A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.
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. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanReference, variant panel and caller settings for the ABO analysis.
ABO reference FASTA (NG_006669.2, 42,144 bp) that reads are aligned to.
string^\S+\.fa(sta)?(\.gz)?$Index (.fai) of the ABO reference FASTA.
string^\S+\.fai$ABO diagnostic variant panel (positions, calling thresholds, ISBT allele associations).
string^\S+\.(yaml|yml|json|csv|tsv)$Panel BED file used as a fallback for the panel-filtering step.
string^\S+\.bed$BED file restricting Clair3 calling (and gVCF reference blocks) to the ABO exon 2-7 region.
string^\S+\.bed$URL of the Clair3 PyTorch model files (pileup.pt and full_alignment.pt) for the sequencing chemistry used.
stringOptional tab-delimited file mapping sequencingID to sampleName to rename samples in the final tables.
stringSkip the optional sample renaming step.
booleantrueParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanBoolean whether to validate parameters against the schema at runtime
booleantrueSuffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when –help or –help_full are provided).
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
booleanCustom 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.
stringLogo shown with the pipeline (defaults to the file set in nextflow.config).
stringBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/