The `fastp` module will zero source FASTQ files if they end in `.fastp.fastq.gz` (data loss scenario)

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

This is due to the logic here:

https://github.com/nf-core/modules/blob/ee5b3472df499c78a4cc3f6b57c4da7cb4d75d25/modules/nf-core/fastp/main.nf#L34

And due to the symlink done here:

https://github.com/nf-core/modules/blob/ee5b3472df499c78a4cc3f6b57c4da7cb4d75d25/modules/nf-core/fastp/main.nf#L82

fastp will get differently-named inputs and outputs, and will end up overwriting (zeroing) the source file. This is a scenario that leads to data loss.

Command used and terminal output

1. Create FASTQ files like `test1_R1.fastp.fastq.gz` and `test_R2.fastp.fastq.gz`. 
2. Run the `fastp` module using these files as input
3. Check the original files
4. The original files  have now 0 bytes in size.

Relevant files

No response

System information

Nextflow 24.10.4
Hardware: HPC
Executor: slurm
Container engine: apptainer
OS: Debian 10

Inspect modules/nf-core/fastp/main.nf at the linked lines 34 and 82, then reproduce the issue with input files ending in .fastp.fastq.gz using the stated Nextflow setup. Done means the module produces its outputs without changing the original FASTQ files, which should retain their contents and nonzero size.