nf-core/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
2.0.0). The latest
stable release is
4.3.1
.
Define where the pipeline should find input data and save output data.
Path to a tsv file providing paths to the fastq files for each sample and the necessary metadata for the analysis.
stringPath to a fasta file containing the C-region primer sequences.
stringPath to a fasta file containinc the V-region primer sequences.
stringPath to the 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})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringDefine the paths to the igblast and IMGT databases if you have them cached.
Path to the cached igblast database.
stringPath to the cached igblast database.
stringSave databases so you can use the cache in future runs.
booleanSpecies to perform Igblast. Choose from: human, mouse.
stringLoci to perform Igblast. Choose from: ig (BCR / Immunoglobulins), tr (TCR).
stringDefine the primer region start and how to deal with the primer alignment.
Protocol used for the V(D)J amplicon sequencing.
stringStart position of V region primers (without counting the UMI barcode).
integerStart position of C region primers (without counting the UMI barcode).
integerPath to fasta file containing the linker sequence, if no V-region primers were used but a linker sequence is present (e.g. 5’ RACE SMARTer TAKARA protocol).
stringIndicate if C region primers are in the R1 or R2 reads.
stringDefine how UMI barcodes should be treated.
Indicate if UMI indices are recorded in a separate index file.
booleanIndicate if UMI indices are recorded in the R1 (default) or R1 fastq file.
stringUMI barcode length in nucleotides.
integer8UMI barcode start position.
integerOptions for the presto tools
Quality threshold for Presto FilterSeq sequence filtering.
integer20Masking mode for the Presto MaskPrimer process. Available: cut, mask, trim, tag.
stringMaximum scoring error for the Presto MaxPrimer process for the C and/or V region primers identification.
number0.2Maximum error for building the primer consensus.
number0.6Define how the B-cell clonal trees should be calculated.
Set to true if to manually adjust the clustering threshold for cell clones.
booleanSet the clustering threshold Hamming distance value.
number0.14Set the method for finding the clustering threshold.
stringdensityDefine downstream analysis options.
Skip repertoire analysis and report generation.
booleanSkip clonal lineage analysis and lineage tree plotting.
booleanSkip multiqc report generation.
booleanOptions for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
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 configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoSet 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+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
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.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
booleanInstead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
boolean