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The distToNearest function within enchantr::enchantr_report function in the task NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:FIND_CLONAL_THRESHOLD returns only NA values for distance as the default value for locusValues within distToNearest is set to "IGH". For TCR data, we expect these values: c("TRA", "TRB", "TRD", "TRG"). It should be made possible to change this parameter in the configuration file.
Command used and terminal output
The pipeline runs without problem with the expected output
Automatic clone_threshold is 'NA'. Consider setting --clonal_threshold manually.
### Relevant files
_No response_
### System information
nextflow version 23.10.1.5891
Hardware: server
Executor: local
Container: singularity
OS: CentOS Linux
nf-core/airrflow version: 4.1
The text was updated successfully, but these errors were encountered:
sorry for the late reply! For TCR data, we expect clones to have the same CDR3, so you can directly set the parameters --clonal_threshold 0, and --skip_report_threshold to skip finding the clonal threshold.
We'll add a check for future versions that this is automatically set for TR locus analysis.
Description of the bug
The distToNearest function within enchantr::enchantr_report function in the task NFCORE_AIRRFLOW:AIRRFLOW:CLONAL_ANALYSIS:FIND_CLONAL_THRESHOLD returns only NA values for distance as the default value for locusValues within distToNearest is set to "IGH". For TCR data, we expect these values: c("TRA", "TRB", "TRD", "TRG"). It should be made possible to change this parameter in the configuration file.
Command used and terminal output
The pipeline runs without problem with the expected output
The command used:
The text was updated successfully, but these errors were encountered: