Multiple uses of seqkit replace module fail due to output/input name conflicts #9647
Description
Have you checked the docs?
Description of the bug
As currently coded seqkit replace module outputs a file named ${meta.id}.${endswith} eg sample1.fasta.
For a one-off usage of seqkit replace this is fine however there is sometimes a need for multiple sequential uses of seqkit replace. In such a situation seqkit replace module is given a file that is named sample1.fasta and will output a file called sample1.fasta. This results in seqkit reporting an error:
[ERRO] input and output files cannot be the same
The solution I think is to stage the input to stop this error from occurring.
Command used and terminal output
Relevant files
No response
System information
No response