nf-core/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.tsv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Specify the processing mode for the pipeline. Available options are "fastq" and "assembled".
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Path to MiAIRR-BioSample mapping
string${projectDir}/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.
stringAvailable protocols are:
specific_pcr_umi: RT-PCR using transcript-specific primers containing UMIs.specific_pcr: RT-PCR using transcript-specific primers.dt_5p_race_umi: 5’-RACE PCR using oligo-dT primers and template switch primers containing UMI.dt_5p_race: 5’-RACE PCR (i.e. RT is followed by a template switch (TS) step) using oligo-dT primers.sc_10x_genomicsgenomics library preparation protocol for scVDJ sequencing.
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).
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.
stringThe pipeline requires UMI barcodes for identifying unique transcripts. These barcodes are typically read from an index file but sometimes can be provided merged with the start of the R1 or R2 reads. If provided in an additional index file, set the --index_file parameter, if provided merged with the R1 or R2 reads, set the --umi_position parameter to R1 or R2, respectively.
UMI 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.
booleanSet to true if UMI barcodes are to be read from a separate Illumina index fastq file. If Illumina indices and UMI barcodes are already integrated into the R1 reads, leave the default --index_file false.
The pipeline requires UMI barcodes for identifying unique transcripts. These barcodes are typically read from an index file but sometimes can be provided merged with the start of the R1 or R2 reads. If provided in an additional index file, set the --index_file parameter, if provided merged with the R1 or R2 reads, set the --umi_position parameter.
Options for adapter trimming and read clipping
Whether to trim adapters in fastq reads with fastp.
booleantrueBy default adapters will be auto-detected, but adapter sequences can also be provided in a fasta file with the --adapter_fasta option.
Fasta file with adapter sequences to be trimmed.
stringNumber 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 error for building the primer consensus in the pRESTO Buildconsensus step.
number0.6Maximum 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.
booleantrueMaximum allowed error for R1 primer alignment.
number0.2Maximum allowed error for R2 primer alignment.
number0.2Align primers instead of scoring them. Used for protocols without primer fixed positions.
booleanMaximum allowed primer length when aligning the primers.
integer50Use MaskPrimers align for a 5' RACE protocol.
booleanIt will align the C-primers with pRESTO MaskPrimers align, and extract the template-switch Oligo and/or linker with defined length in --primer_r2_extract_len.
Use when primer sequences are unknown but when their approximate positions are known.
booleanUse in combination with --primer_r1_extract_len and --primer_r2_extract_len to define the sequence regions to cut corresponding to the approximate unknown primer sequence length prior to alignment. It is also possible to define a UMI barcode for extraction if it's position is unknown.
R1 primer extract length when using --maskprimers_extract.
integerR2 primer extract length when using --maskprimers_extract.
integerUse AssemblePairs sequential instead of AssemblePairs align when assembling read pairs.
booleanAlign internal C-region for a more precise isotype characterization.
booleanProvide internal C-region sequences for a more precise C-region characterization. Then also set the align_cregion flag.
stringMaximum allowed length when aligning the internal C-region.
integer100Maximum allowed error when aligning the internal C-region.
number0.3Mask mode for C-region alignment.
stringtagSkip 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.
booleanOptions specific for raw unselected RNA-seq input.
Specifies which read holds the barcodes
stringfile containing the barcodes
Indicate if UMI indices are recorded in the R1 (default) or R1 fastq file.
stringfile containing 10x Genomics-like UMIs
Specifies where in the read the barcodes and UMIs can be found.
stringFor further information see the TRUST4 docs.
Options 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.
booleantruePath to the germline reference fasta.
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zipBy default, we provide a pre-downloaded version of the IMGT database. It is also possible to provide a custom reference fasta database. To fetch a fresh version of IMGT, set the --fetch_imgt parameter instead.
Path to the cached igblast database.
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zipBy default, we provide a pre-downloaded version of the IMGT database. It is also possible to provide a custom reference fasta database. To fetch a fresh version of IMGT, set the --fetch_imgt parameter instead.
Set this flag to fetch the IMGT reference data at runtime.
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,numberautoPerform clonal lineage tree analysis.
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_idLineage tree software to use to build trees within Dowser. If you change the default, also set the lineage_tree_exec parameter.
stringPath to lineage tree building executable.
string/usr/local/bin/raxml-ngName 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.
booleanSkip report of EnchantR FindThreshold for all samples together.
booleanSkip all clonal anlaysis processes
booleanOptions to generate BCR and TCR embeddings with Amulety
Generate a sequence amino acid translation with IgBlast.
booleanGenerate sequence embeddings with amulety.
string^((antiberta2|antiberty|balmpaired|esm2)?,?)*(?<!,)$Provide a comma separated list of the embeddings to generate (e.g. antiberty,antiberta2 ). Currently supported embeddings are:
- BCR embeddings: antiberta2, antiberty, balmpaired.
- Unspecific embeddings: esm2.
BCR or TCR chains to include for embedding.
stringHProvide "H" for heavy chain only (BCR: IGH, TCR: TRB, TRD), or "HL" for heavy and light chain (requires single-cell paired data with the column "cell_id"). Cells with only heavy chains will be removed prior to embedding when HL is selected.
Use GPU to generate embeddings.
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.
Do not load the iGenomes reference config.
booleantrueDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters 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/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/airrflow/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string