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Fix csv generation #185

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Fix csv generation #185

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LouisLeNezet
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@LouisLeNezet LouisLeNezet commented Feb 20, 2025

This PR should solve the different csv issues

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/phaseimpute 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>).
  • 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).

@LouisLeNezet LouisLeNezet self-assigned this Feb 20, 2025
@LouisLeNezet LouisLeNezet added the bug Something isn't working label Feb 20, 2025
@LouisLeNezet LouisLeNezet added this to the v1.1.0 milestone Feb 20, 2025
This was linked to issues Feb 20, 2025
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@atrigila atrigila left a comment

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Should the csv pointing to chunks be updated as well?

        // Chunks
        exportCsv(
            VCF_CHUNK_GLIMPSE.out.chunks.map{ meta, file ->
                [meta, [2:"prep_panel/chunks"], file]
            },
            ["id", "chr"], "panel,chr,file",
            "chunks.csv", "prep_panel/csv"
        )
    }
    ```

@LouisLeNezet
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Should the csv pointing to chunks be updated as well?

        // Chunks
        exportCsv(
            VCF_CHUNK_GLIMPSE.out.chunks.map{ meta, file ->
                [meta, [2:"prep_panel/chunks"], file]
            },
            ["id", "chr"], "panel,chr,file",
            "chunks.csv", "prep_panel/csv"
        )
    }
    ```

It is already updated to

// Chunks
exportCsv(
    VCF_CHUNK_GLIMPSE.out.chunks.map{ meta, file ->
        [meta, [2:"prep_panel/chunks/glimpse1"], file]
    },
    ["id", "chr"], "panel,chr,file",
    "chunks_glimpse1.csv", "prep_panel/csv"
)

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Csv output file Wrong samplesheet generation
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