+ ## 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...
Description of the bug
The patch is command is faulty:
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