PORECHOP_ABI patch (on bouncy_basenji dev branch) overwrites input

[jfy133]

Description of the bug

The patch is command is faulty:

+     ## To ensure ID matches rest of pipeline based on meta.id rather than input file name
+
+    [[ -f ${prefix}.fastq.gz   ]] || ln -s $reads ${prefix}.fastq.gz

This will symlink is fine, but then the symlinked input file can be then the same as the output file, so overwrites itself to the original file, rather than a new file...

Command used and terminal output

No response

Relevant files

No response

System information

No response