Autorenaming of files in new cellranger module leads to erroneous renaming of sample ID containing R1 in it, like in SRR ids

[BurtonChia]

Description of the bug

When running scrnaseq v 2.4.0 with the new cellranger #246 , we are encountering errors like this. This happens on all samples starting with SRR1xxx.

AssertionError: We expect R1 and R2 of the same sample to have the same filename except for R1/R2.
  Files involved:
      - fastq_001/SRR14923965_S1_L001_R1_001.fastq.gz
      - fastq_002/SRR14923965_S1_L001_R2_001.fastq.gz

A look at the command indicates the error is due to how the renaming of r1.name for the comparison for r2.name, in particular:
if r1.name.replace("R1", "R2") != r2.name:

Instead, this line should read: if r1.name.replace("_R1_", "_R2_") != r2.name: to ensure sample IDs containing "R1" in them don't get renamed by mistake.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[grst]

Thanks for reporting, this should already be fixed on dev
See #261

Would be great if you could give it a try!

[BurtonChia]

That's great! We'll give the dev build a run and report back the results.