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Added IRIDA Next JSON output file #10

Merged
merged 1 commit into from
Jun 10, 2024
Merged

Added IRIDA Next JSON output file #10

merged 1 commit into from
Jun 10, 2024

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sgsutcliffe
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Added in the iridanext plugin and a iridanext.config to format output JSON for IRIDA-Next compatibility. Included all output files per sample.

  • detailed_summary.tsv
    - mlst.tsv
    - plasmidfinder.tsv
    - resfinder.tsv
    - results.xlsx
    - settings.txt
    - summary.tsv

No global or meta information added.

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/staramr branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@sgsutcliffe sgsutcliffe requested a review from apetkau June 7, 2024 17:26
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This looks great Steven. Thanks 😄 . Just one comment, which is unrelated to changes you've made but I just noticed it and so we should fix it.

@@ -179,8 +179,10 @@ singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
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Could you change nf-validation to [email protected] so that we are using a fixed version.

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Will do!

@sgsutcliffe sgsutcliffe merged commit b353f27 into dev Jun 10, 2024
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@sgsutcliffe sgsutcliffe deleted the add-iridanext-plugin branch June 11, 2024 13:53
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2 participants