github.com/nf-core/bcellmagic

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
  -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.

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