B cell repertoire analysis pipeline with immcantation framework. Usage: The typical command for running the pipeline is as follows: nextflow run nf-core/bcellmagic --reads '*_R{1,2}.fastq.gz' -profile standard,docker Mandatory arguments: --cprimers Path to CPrimers FASTA File --vprimers Path to VPrimers FASTA File --metadata Path to Metadata TSV --umi_length Length of UMI barcodes -profile Configuration profile to use. Can use multiple (comma separated) Available: standard, conda, docker, singularity, awsbatch, test Options: References: If not specified in the configuration file or you wish to overwrite any of the references. --imgtdb_base Path to predownloaded imgtDB --igblast_base Path to predownloaded igblastDB Define clones: --set_cluster_threshold Set this parameter to allow manual hamming distance threshold for cell cluster definition. --cluster_threshold Once set_cluster_threshold is true, set cluster_threshold value (float). Index file: --index_file If the unique molecular identifiers (UMI) are available in a separate index file, merge it to R1 reads. --umi_position If UMI are not available in a separate index file, but already merged with the R1, and R2 reads, speciffy position (R1/R2). Repertoire downstream analysis: --downstream_only If tables are provided in option `--changeo_tables`, then perform only cluster and repertoire analysis steps. --changeo_tables Provide Changeo table in '.tsv' if only downstream analysis is desired. --skipDownstream Skip downstream clonal and repertoire analysis steps. Other options: --outdir The output directory where the results will be saved --email 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 --maxMultiqcEmailFileSize Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB) -name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. AWSBatch options: --awsqueue The AWSBatch JobQueue that needs to be set when running on AWSBatch --awsregion The AWS Region for your AWS Batch job to run on