Bulk RNAseq pcr_target_locus specification

Description of the bug

Thanks for the great tool, it offers a really wide range of analysis in a convenient way! I would like to analyze bulk (untargeted) blood RNAseq data using your pipeline. To do this, I ran MIXCR in RNAseq mode to generate airr files, which I fed into the airrflow pipeline.

However, I am unsure what to use as "pcr_target_locus" for the assembled input sample sheet since I do not have a specific target locus? How important is this parameter and will different tools and output be generated based on it?

Specifying "pcr_target_locus" as "IG" works fine, but will I miss the TCR analysis? When I specified both "IG" and "TR" in two lines for each sample, I got the error attached at the end.

Could you advise if bulk "normal" RNAseq analysis is suitable for your pipeline at all, or would you recommend against it? Thanks in advance.

Command used and terminal output

nextflow run nf-core/airrflow -r 3.2.0 -profile docker --mode assembled --input samplesheet.tsv --outdir airr_output

-[nf-core/airrflow] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:DOWSER_LINEAGES (subject2)'

Caused by:
  Process `NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:DOWSER_LINEAGES (subject2)` terminated with an error exit status (1)

Command executed:

  Rscript -e "enchantr::enchantr_report('dowser_lineage', \
                                          report_params=list('input'='subject2__clone-pass.tsv', \
                                          'exec'='/usr/local/share/igphyml/src/igphyml', \
                                          'outdir'=getwd(), \
                                          'nproc'=10,\
                                          'log'='subject2_dowser_command_log' ,'build'='igphyml','minseq'=5,'tips'='c_call','traits'='c_call'))"

      cp -r enchantr subject2_dowser_report && rm -rf enchantr

      echo "NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:DOWSER_LINEAGES": > versions.yml
      Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'
  '))" >> versions.yml

Command exit status:
  1

Command output:
  1/18                   
  2/18 [global-options]  
  3/18                   
  4/18 [input-parameters]
  5/18 [unnamed-chunk-1] 
  6/18                   
  7/18 [read-repertoires]
  8/18                   
  9/18 [formatClones]    

Command error:

  processing file: _main.Rmd
  1/18                   
  2/18 [global-options]  
  3/18                   
  4/18 [input-parameters]
  5/18 [unnamed-chunk-1] 
  6/18                   
  7/18 [read-repertoires]
  8/18                   
  9/18 [formatClones]    

  Quitting from lines 153-206 [formatClones] (_main.Rmd)
  Error:
  ! multiple heavy chain locus found.
  Warning messages:
  1: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'enchantr' 
  2: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'enchantr' 
  3: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'enchantr' 
  Execution halted

Relevant files

samplesheet.tsv.zip

System information

Nextflow version: 23.10.1 Hardware: Desktop Executor: local Container engine: Docker OS: Ubuntu 20.04.6 LTS Version of nf-core/airrflow: 3.2.0

nf-core / airrflow