nf-core/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
3.0). 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.
stringSpecify the processing mode for the pipeline. Available options are “fastq” and “assembled”.ptions are: ‘raw’
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})$Path to MiAIRR-BioSample mapping
stringbcellmagic/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsvExperimental 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 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 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.
integerIndicate if UMI indices are recorded in a separate index file.
booleanOptions for adapter trimming and read clipping
Whether to trim adapters in fastq reads with fastp.
booleantrueFasta file with adapter sequences to be trimmed.
stringNoneNumber of bases to clip 5’ in R1 reads.
integerNumber of bases to clip 5’ in R2 reads.
integerNumber of bases to clip 3’ in R1 reads.
integerNumber of bases to clip 3’ in R2 reads.
integerTrim adapters specific for Nextseq sequencing
booleanOption to save trimmed reads.
booleanOptions for the pRESTO sequence assembly processes
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.
booleantrueOptions for the VDJ annotation processes.
Whether to reassign genes if the input file is an AIRR formatted tabulated file.
booleantrueSubset to productive sequences.
booleantrueSave databases so you can use the cache in future runs.
booleanPath to the cached IMGT database.
stringPath to the cached igblast database.
stringUse this flag for directly calling IgBlast for reference alignment, instead of using the changeo assigngenes and changeo makedb options that call IgBlast in the background. Allows for additional configuration of the IgBlast call.
booleanOptions for bulk sequence filtering after VDJ assignment.
Name of the field used to collapse duplicated sequences.
stringsample_idWhether to run the process to detect contamination.
booleanWhether to apply the chimera removal filter.
booleanDefine how the B-cell clonal trees should be calculated.
Set the clustering threshold Hamming distance value. Default: ‘auto’
string,numberautoSkip clonal lineage analysis and lineage tree plotting.
booleanName of the field used to group data files to identify clones.
stringsubject_idName of the field used to identify external groups used to identify a clonal threshold.
stringsubject_idPath to IgPhyml executable.
string/usr/local/share/igphyml/src/igphymlName of the field used to determine if a sample is single cell sequencing or not.
stringsingle_cellSkip report of EnchantR DefineClones for all samples together.
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.pngCustom logo for the EnchantR reports.
string${projectDir}/assets/nf-core-airrflow_logo_reports.pngSkip repertoire analysis and report generation.
booleanSkip multiqc report.
booleanOptions for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleantrueParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringDirectory to keep pipeline Nextflow logs and reports.
string${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.
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})$Send plain-text email instead of HTML.
booleanMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom 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.
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
boolean