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

[PCQuilis]

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]

Fixed by #1052