Mulitmapping reads dropped resulting in empty output files using GRCh37

[nick-phillips]

Description of the bug

I ran the pipeline using genome GRCh37 and found no integration sites in my samples, despite a large number of reads aligned to virus. Tracing the intermediate output, I saw that empty files were written in the insertion_site_candidates.nf module.

I believe the issue occurs here:

viralintegration/bin/greedily_assign_multimapping_reads_among_insertions.py

Line 77 in 70e558a

(re.match("chr[\dMXY]+$", row["chrA"]) is not None) ^ (re.match("chr[\dMXY]+$", row["chrB"]) is not None)

Using --genome GRCh37, the Ensembl reference contigs do not contain chr, so everything is dropped. I am rerunning now with GRCh38 to verify that I can detect integration sites.

Command used and terminal output

$ nextflow nf-core/viralintegration --input <sample_sheet.csv> --outdir <output_path> --genome GRCh37 -profile singularity

Relevant files

No response

System information

No response