Input and Output file names were the same

[dorotejavujinovic]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[jemten]

Hello @dorotejavujinovic 👋
Thanks for taking an interest in the pipeline. Have you experienced issues from this module? When possible we try to leave the file naming to the config so that the user/developer can choose the name of the output file. As this is an nf-core module we also try to do these kind of updates to the nf-core/modules repo and then install teh new module here.