nf-core/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
2.3.0). The latest
stable release is
4.3.1
.
Define where the pipeline should find input data and save output data.
Specify the subworkflow to be executed.
stringPath to a tsv file providing paths to the fastq files for each sample and the necessary metadata for the analysis.
stringThe 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})$Experimental protocol used to generate the data
Protocol used for the V(D)J amplicon sequencing library generation.
stringPath 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).
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.
booleanDefine the primer region start and how to deal with the primer alignment.
Path to a fasta file containinc the V-region primer sequences.
stringPath to a fasta file containing the C-region primer sequences.
stringStart position of V region primers (without counting the UMI barcode).
integerStart position of C region primers (without counting the UMI barcode).
integerIndicate if C region primers are in the R1 or R2 reads.
stringSpecify to match the tail-end of the sequence against the reverse complement of the primers. This also reverses the behavior of the —start argument, such that start position is relative to the tail-end of the sequence. (default: False)Maximum scoring error for the Presto MaxPrimer process for the C and/or V region primers identification.
booleanDefine 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. Set to 0 if no UMIs present.
integer-1UMI barcode start position in the index read.
integerOptions for the presto tools
Quality threshold for Presto FilterSeq sequence filtering.
integer20Maximum primer scoring error in the Presto MaskPrimer step for the C and/or V region primers identification.
number0.2Maximum error for building the primer consensus in the Presto Buildconsensus step.
number0.6Masking mode for the Presto MaskPrimer step. Available: cut, mask, trim, tag.
stringMaximum error for building the sequence consensus in the Presto BuildConsensus step.
number0.1Maximum gap for building the sequence consensus in the Presto BuildConsensus step.
number0.5Cluster sequences by similarity regardless of any annotation with Presto ClusterSets and annotate the cluster ID additionally to the UMI barcode.
booleantrueDefine 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
booleanCustom report Rmarkdown file.
string${projectDir}/assets/repertoire_comparison.RmdCustom report style file in css format.
string${projectDir}/assets/nf-core_style.cssCustom logo for the report.
string${projectDir}/assets/nf-core-airrflow_logo_light.pngOptions for software packaging
Enable conda to run pipeline with conda environment.
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 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.
booleanMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringFile 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
booleanArguments for this subworkflow
Name of the field used to collapse duplicated sequences
stringfilename,cell_idName of the field used to group data files to identify clones
stringsubject_idWhether to reassign genes if the input file is an AIRR formatted tabulated file
booleantrueSubset to productive sequences
booleantrueWhether to apply the chimera removal filter
booleantrueUse auto to automatically set a threshold to identify clonally related sequences. Set
string,numberautoPath to MiAIRR-BioSample mapping
stringbcellmagic/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsvWhether input samples include single cell sequencing samples
stringsingle_cell