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.
string
Specify the processing mode for the pipeline. Available options are “fastq” and “assembled”.ptions are: ‘raw’
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})$
Path to MiAIRR-BioSample mapping
string
bcellmagic/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv
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 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 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
Indicate if UMI indices are recorded in a separate index file.
boolean
Options for adapter trimming and read clipping
Whether to trim adapters in fastq reads with fastp.
boolean
true
Fasta file with adapter sequences to be trimmed.
string
None
Number of bases to clip 5’ in R1 reads.
integer
Number of bases to clip 5’ in R2 reads.
integer
Number of bases to clip 3’ in R1 reads.
integer
Number of bases to clip 3’ in R2 reads.
integer
Trim adapters specific for Nextseq sequencing
boolean
Option to save trimmed reads.
boolean
Options for the pRESTO sequence assembly processes
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
Options for the VDJ annotation processes.
Whether to reassign genes if the input file is an AIRR formatted tabulated file.
boolean
true
Subset to productive sequences.
boolean
true
Save databases so you can use the cache in future runs.
boolean
Path to the cached IMGT database.
string
Path to the cached igblast database.
string
Use 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.
boolean
Options for bulk sequence filtering after VDJ assignment.
Name of the field used to collapse duplicated sequences.
string
sample_id
Whether to run the process to detect contamination.
boolean
Whether to apply the chimera removal filter.
boolean
Define how the B-cell clonal trees should be calculated.
Set the clustering threshold Hamming distance value. Default: ‘auto’
string,number
auto
Skip clonal lineage analysis and lineage tree plotting.
boolean
Name of the field used to group data files to identify clones.
string
subject_id
Name of the field used to identify external groups used to identify a clonal threshold.
string
subject_id
Path to IgPhyml executable.
string
/usr/local/share/igphyml/src/igphyml
Name of the field used to determine if a sample is single cell sequencing or not.
string
single_cell
Skip report of EnchantR DefineClones for all samples together.
boolean
Custom report Rmarkdown file.
string
${projectDir}/assets/repertoire_comparison.Rmd
Custom report style file in css format.
string
${projectDir}/assets/nf-core_style.css
Custom logo for the report.
string
${projectDir}/assets/nf-core-airrflow_logo_light.png
Custom logo for the EnchantR reports.
string
${projectDir}/assets/nf-core-airrflow_logo_reports.png
Skip repertoire analysis and report generation.
boolean
Skip multiqc report.
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
Display version and exit.
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
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
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