Input BAM files overwritten and emptied when using same filename as ID

nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

https://nf-co.re/eager

MIT License

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Input BAM files overwritten and emptied when using same filename as ID #1051

Closed PCQuilis closed 7 months ago

PCQuilis commented 7 months ago

Check Documentation

I have checked the following places for your error:

[] nf-core website: troubleshooting
[] nf-core/eager pipeline documentation
- nf-core/eager FAQ/troubleshooting can be found here

Description of the bug

Eager pipeline overwrites my input BAM files with empty files at the samtools filter step, when using the same file name as the output of this step when providing unmapped files.

TCLamnidis commented 7 months ago

Fixed by #1052