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Seqkit replace - fix #9647 and #9646#12213

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ammaraziz wants to merge 3 commits into
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ammaraziz:seqkit-update
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Seqkit replace - fix #9647 and #9646#12213
ammaraziz wants to merge 3 commits into
nf-core:masterfrom
ammaraziz:seqkit-update

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@ammaraziz

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Round 2 of for this - previous PR: #9686

Closes #9647 and #9646

In hindsight didnt need to make issues but a force of habit.

Incorporated the comments from the two reviewers.

@SPPearce SPPearce left a comment

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Can you please add the disambiguation check, to ensure that the input/output files are not the same (if the default prefix is overridden)

@atrigila atrigila added the awaiting-changes will be closed after 30 days label Jul 2, 2026
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Multiple uses of seqkit replace module fail due to output/input name conflicts

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