search

nf-core / airrflow

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
https://nf-co.re/airrflow
MIT License
54 stars 34 forks source link

Incorrect number of sequences #340

Open eba28 opened 4 months ago

eba28 commented 4 months ago

Description of the bug

One of my samples didn't have any sequence pass through the SingleCellQC step. Instead of showing a 0 for the sequence count in the summary report, it instead shows some other larger number (it may have copied the sequence count of the last sample or it's a coincidence that they are the same). There is no tsv file for that sample in results/qc-filtering/single-cell-qc/all_reps_scqc_report/repertoires.

Command used and terminal output

nextflow run nf-core/airrflow -r 4.1.0 -profile docker --input [my_local_path]/airrflow_bcr.tsv --mode assembled --outdir results --reassign --productive_only --clonal_threshold 0.18 --cloneby subject_id --max_cpus 10 -c custom.config

Relevant files

No response

System information