nf-core/airrflow

The input file includes important sample metadata and the path to the R1 and R2 fastq files, and index read file (I), if available. The file should include the following columns, separated with tabs, with exactly these header names:

ID Source Treatment Extraction_time Population R1 R2 I1  
QMKMK072AD Patient_2 Drug_treatment baseline p sample_S8_L001_R1_001.fastq.gz sample_S8_L001_R2_001.fastq.gz sample_S8_L001_I1_001.fastq.gz  

This metadata will then be automatically annotated in a column with the same header in the tables outputed by the pipeline. Where:

• ID: sample ID.
• Source: patient or organism code.
• Treatment: treatment condition applied to the sample.
• Extraction_time: time of cell extraction for the sample.
• Population: B-cell population (e.g. naive, double-negative, memory, plasmablast).
• R1: path to fastq file with first mates of paired-end sequencing.
• R2: path to fastq file with second mates of paired-end sequencing.
• I1: path to fastq with illumina index and UMI (unique molecular identifier) barcode (optional column)

Specify the path for your input file like this:

--input 'path/to/metadata/metadata_sheet.tsv'  

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.

Available 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.

If it is not provided, the database will be newly downloaded.

If it is not provided, the database will be newly downloaded.

Set 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.

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 to R1 or R2, respectively.

By default adapters will be auto-detected, but adapter sequences can also be provided in a fasta file with the --adapter_fasta option.

The primer masking modes will perform the following actions:

• cut: remove both the primer region and the preceding sequence.
• mask: replace the primer region with Ns and remove the preceding sequence.
• trim: remove the region preceding the primer, but leave the primer region intact.
• tag: leave the input sequence unmodified.

Set the --set_cluster_threshold parameter to allow manual cluster hamming distance threshold definition. Then specify the value in the --cluster_threshold parameter.

By default, the pipeline will define clones for each of the samples, as two sequences having the same V gene assignment, C gene assignment, J-gene assignment, and junction length. Additionally, the similarity of the junction region sequences will be assessed by hamming distances. A distance threshold for determining if two sequences come from the same clone is automatically determined by the process shazam. Alternatively, a hamming distance threshold can be manually set by setting the --set_cluster_threshold and --cluster_threshold parameters.

To have any effect, the --set_cluster_threshold parameter needs to be set to true.

By default, the pipeline will define clones for each of the samples, as two sequences having the same V gene assignment, C gene assignment, J-gene assignment, and junction length. Additionally, the similarity of the junction region sequences will be assessed by hamming distances. A distance threshold for determining if two sequences come from the same clone is automatically determined by the process shazam. Alternatively, a hamming distance threshold can be manually set by setting the --set_cluster_threshold and --cluster_threshold parameters.

This method will be used to find the Hamming nearest neighbor distances threshold for determining if a sequence belongs to the same B/T-cell clone or not. Available methods are "gmm" for a maximum-likelihood Gamma or Gaussian mixture fitting, and "density" for fitting a binned approximation to the ordinary kernel density estimate to the nearest neighbor distances.