Multiple uses of seqkit replace module fail due to output/input name conflicts
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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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the seqkit replace module in the nf-core/modules repository and reproduce the sequential-use case described in the issue. Confirm that repeated use can stage the input so seqkit no longer receives identical input and output names; the issue provides no specific test or file path to verify.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100