Seqkit replace - fix #9647 and #9646

[ammaraziz]

PR checklist

Closes #9647 and #9646

1. Multiple uses of seqkit replace module fail due to output/input name conflicts #9647 fix by staging the input as "raw.fasta" so that subsequent uses don't fail.
2. seqkit replace incorrectly uses the '-i' flag #9646 remove -i flag incorrectly used as input, -i for ignoring case.

[SPPearce]

We normally catch cases where the input file can be the same as the output file in this way:
https://github.com/search?q=repo%3Anf-core%2Fmodules%20disambig&type=code
Which can be combined with setting a default value for prefix that isn't just meta.id, e.g.
def prefix = task.ext.prefix ?: "${meta.id}_replaced