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.

required
type: string

Specify the processing mode for the pipeline. Available options are “fastq” and “assembled”.ptions are: ‘raw’

type: string

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Path to MiAIRR-BioSample mapping

type: string
default: 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.

type: 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).

type: 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.

type: string

Path to a fasta file containing the C-region primer sequences.

type: string

Start position of V region primers (without counting the UMI barcode).

type: integer

Start position of C region primers (without counting the UMI barcode).

type: integer

Indicate if C region primers are in the R1 or R2 reads.

type: 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.

type: boolean

Define how UMI barcodes should be treated.

Indicate if UMI indices are recorded in the R1 (default) or R1 fastq file.

type: string

UMI barcode length in nucleotides. Set to 0 if no UMIs present.

type: integer
default: -1

UMI barcode start position in the index read.

type: integer

Indicate if UMI indices are recorded in a separate index file.

type: boolean

Options for adapter trimming and read clipping

Whether to trim adapters in fastq reads with fastp.

type: boolean
default: true

Fasta file with adapter sequences to be trimmed.

type: string
default: None

Number of bases to clip 5’ in R1 reads.

type: integer

Number of bases to clip 5’ in R2 reads.

type: integer

Number of bases to clip 3’ in R1 reads.

type: integer

Number of bases to clip 3’ in R2 reads.

type: integer

Trim adapters specific for Nextseq sequencing

type: boolean

Option to save trimmed reads.

type: boolean

Options for the pRESTO sequence assembly processes

Quality threshold for pRESTO FilterSeq sequence filtering.

type: integer
default: 20

Maximum primer scoring error in the pRESTO MaskPrimer step for the C and/or V region primers identification.

type: number
default: 0.2

Maximum error for building the primer consensus in the pRESTO Buildconsensus step.

type: number
default: 0.6

Masking mode for the pRESTO MaskPrimer step. Available: cut, mask, trim, tag.

type: string

Maximum error for building the sequence consensus in the pRESTO BuildConsensus step.

type: number
default: 0.1

Maximum gap for building the sequence consensus in the pRESTO BuildConsensus step.

type: number
default: 0.5

Cluster sequences by similarity regardless of any annotation with pRESTO ClusterSets and annotate the cluster ID additionally to the UMI barcode.

type: boolean
default: true

Options for the VDJ annotation processes.

Whether to reassign genes if the input file is an AIRR formatted tabulated file.

type: boolean
default: true

Subset to productive sequences.

type: boolean
default: true

Save databases so you can use the cache in future runs.

type: boolean

Path to the cached IMGT database.

type: string

Path to the cached igblast database.

type: 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.

type: boolean

Options for bulk sequence filtering after VDJ assignment.

Name of the field used to collapse duplicated sequences.

type: string
default: sample_id

Whether to run the process to detect contamination.

type: boolean

Whether to apply the chimera removal filter.

type: boolean

Define how the B-cell clonal trees should be calculated.

Set the clustering threshold Hamming distance value. Default: ‘auto’

type: string,number
default: auto

Skip clonal lineage analysis and lineage tree plotting.

type: boolean

Name of the field used to group data files to identify clones.

type: string
default: subject_id

Name of the field used to identify external groups used to identify a clonal threshold.

type: string
default: subject_id

Path to IgPhyml executable.

type: string
default: /usr/local/share/igphyml/src/igphyml

Name of the field used to determine if a sample is single cell sequencing or not.

type: string
default: single_cell

Skip report of EnchantR DefineClones for all samples together.

type: boolean

Custom report Rmarkdown file.

type: string
default: ${projectDir}/assets/repertoire_comparison.Rmd

Custom report style file in css format.

type: string
default: ${projectDir}/assets/nf-core_style.css

Custom logo for the report.

type: string
default: ${projectDir}/assets/nf-core-airrflow_logo_light.png

Custom logo for the EnchantR reports.

type: string
default: ${projectDir}/assets/nf-core-airrflow_logo_reports.png

Skip repertoire analysis and report generation.

type: boolean

Skip multiqc report.

type: boolean

Options for the reference genome indices used to align reads.

Directory / URL base for iGenomes references.

hidden
type: string
default: s3://ngi-igenomes/igenomes

Do not load the iGenomes reference config.

hidden
type: boolean
default: true

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${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.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|day)\s*)+$

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean