nf-core/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
2.1.0
). 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.
string
Path to a tsv file providing paths to the fastq files for each sample and the necessary metadata for the analysis.
string
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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.
string
Path 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).
string
Define the paths to the igblast and IMGT databases if you have them cached.
Path to the cached igblast database.
string
Path to the cached igblast database.
string
Save databases so you can use the cache in future runs.
boolean
Species to perform Igblast. Choose from: human, mouse.
string
Define the primer region start and how to deal with the primer alignment.
Path to a fasta file containinc the V-region primer sequences.
string
Path to a fasta file containing the C-region primer sequences.
string
Start position of V region primers (without counting the UMI barcode).
integer
Start position of C region primers (without counting the UMI barcode).
integer
Indicate if C region primers are in the R1 or R2 reads.
string
Specify 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.
boolean
Define how UMI barcodes should be treated.
Indicate if UMI indices are recorded in a separate index file.
boolean
Indicate if UMI indices are recorded in the R1 (default) or R1 fastq file.
string
UMI barcode length in nucleotides. Set to 0 if no UMIs present.
integer
-1
UMI barcode start position in the index read.
integer
Options for the presto tools
Quality threshold for Presto FilterSeq sequence filtering.
integer
20
Maximum primer scoring error in the Presto MaskPrimer step for the C and/or V region primers identification.
number
0.2
Maximum error for building the primer consensus in the Presto Buildconsensus step.
number
0.6
Masking mode for the Presto MaskPrimer step. Available: cut, mask, trim, tag.
string
Maximum error for building the sequence consensus in the Presto BuildConsensus step.
number
0.1
Maximum gap for building the sequence consensus in the Presto BuildConsensus step.
number
0.5
Cluster sequences by similarity regardless of any annotation with Presto ClusterSets and annotate the cluster ID additionally to the UMI barcode.
boolean
true
Define how the B-cell clonal trees should be calculated.
Set to true if to manually adjust the clustering threshold for cell clones.
boolean
Set the clustering threshold Hamming distance value.
number
0.14
Set the method for finding the clustering threshold.
string
density
Define downstream analysis options.
Skip repertoire analysis and report generation
boolean
Skip clonal lineage analysis and lineage tree plotting.
boolean
Skip multiqc report
boolean
Options for software packaging
Enable conda to run pipeline with conda environment.
boolean
Options for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
true
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Arguments for this subworkflow
Name of the field used to collapse duplicated sequences
string
filename,cell_id
Name of the field used to group data files to identify clones
string
subject_id
Whether to reassign genes if the input file is an AIRR formatted tabulated file
boolean
true
Subset to productive sequences
boolean
true
Whether to apply the chimera removal filter
boolean
true
Use auto
to automatically set a threshold to identify clonally related sequences. Set
string,number
auto
Path to MiAIRR-BioSample mapping
string
bcellmagic/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv
Whether input samples include single cell sequencing samples
string
single_cell