nf-core/airrflow

Path to comma-separated file containing information about the samples in the experiment.

Specify the processing mode for the pipeline. Available options are “fastq” and “assembled”.

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

Email address for completion summary.

Path to MiAIRR-BioSample mapping

Whether to save repertoires in each intermediate step

Save only repertoire file and summary report by default. If set the value to be true, full cellranger results including bam, fasta and fastq files will be saved in the output folder.

Protocol used for the V(D)J amplicon sequencing library generation.

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).

Path to a fasta file containinc the V-region primer sequences.

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

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

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

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

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.

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

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

UMI barcode start position in the index read.

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

Whether to trim adapters in fastq reads with fastp.

Fasta file with adapter sequences to be trimmed.

Number of bases to clip 5’ in R1 reads.

Number of bases to clip 5’ in R2 reads.

Number of bases to clip 3’ in R1 reads.

Number of bases to clip 3’ in R2 reads.

Trim adapters specific for Nextseq sequencing

Option to save trimmed reads.

Quality threshold for pRESTO FilterSeq sequence filtering.

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

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

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

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

Maximum allowed error for R1 primer alignment.

Maximum allowed error for R2 primer alignment.

Align primers instead of scoring them. Used for protocols without primer fixed positions.

Maximum allowed primer length when aligning the primers.

Masking mode for R1 primers.

Masking mode for R2 primers.

Use MaskPrimers align for a 5’ RACE protocol.

Use when primer sequences are unknown but when their approximate positions are known.

R1 primer extract length when using --maskprimers_extract.

R2 primer extract length when using --maskprimers_extract.

Use AssemblePairs sequential instead of AssemblePairs align when assembling read pairs.

Align internal C-region for a more precise isotype characterization.

Provide internal C-region sequences for a more precise C-region characterization. Then also set the align_cregion flag.

Maximum allowed length when aligning the internal C-region.

Maximum allowed error when aligning the internal C-region.

Mask mode for C-region alignment.

Skip filter step after alignment that ensures that locus should match the v_call chain, the sequence alignment should have at least 200 informative positions (excluding N or gaps), and maximum 10% N nucleotides in the alignment.

Path to the reference directory required by cellranger. Can either be directory or tar.gz.

Specifies which read holds the barcodes

Indicate if UMI indices are recorded in the R1 or R2 fastq file.

Specifies where in the read the barcodes and UMIs can be found.

path to the barcode whitelist.

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

Subset to productive sequences.

Save germline database to reuse the cache in future runs.

Path to the germline reference fasta.

Path to the cached igblast database.

Fetch the selected germline reference bundle at runtime instead of using cached reference inputs.

Name of the field used to collapse duplicated sequences.

Whether to run the process to detect contamination.

Whether to apply the chimera removal filter.

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

Perform clonal lineage tree analysis.

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

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

Lineage tree software to use to build trees within Dowser. If you change the default, also set the lineage_tree_exec parameter.

Path to lineage tree building executable.

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

Skip report of EnchantR DefineClones for all samples together.

Skip report of EnchantR FindThreshold for all samples together.

Skip all clonal analysis processes

Perform TIgGER novel allele and genotype inference.

Name of the field used to group data files to infer genotype.

Threshold for determining if two sequences come from the same clone or not.

Keep only one representative sequence per clone to perform genotype inference.

Perform TIgGER novel allele inference.

Generate a sequence amino acid translation with IgBlast.

Generate sequence embeddings with amulety.

BCR or TCR chains to include for embedding.

Use GPU to generate embeddings.

Custom report Rmarkdown file.

Custom report style file in css format.

Custom logo for the report.

Custom logo for the EnchantR reports.

Skip repertoire analysis and report generation.

Skip multiqc report.

Display the help message.

Display the full detailed help message.

Display hidden parameters in the help message (only works when –help or –help_full are provided).