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Major pipeline rewrite to use DSL2 with shared [nf-core/modules](https://github.com/nf-core/modules).
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> **Warning:** Breaking change!
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> The pipeline now requires a sample sheet to be passed to the pipeline with `--input`:
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> | sample | fastq_1 | fastq_2 | genome |
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> | ------ | ------- | ------- | ------ |
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> See an example [here](https://github.com/nf-core/test-datasets/blob/methylseq/samplesheet.csv)
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> The `genome` column is not yet used but will give the ability to map to multiple genomes in a single run in a future release. See [#181](https://github.com/nf-core/methylseq/issues/181).
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>
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> Supplying the reference geneome with `--genome` as before works as usual.
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> **Warning**: Breaking change! ⚠️
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The pipeline now requires a sample sheet to be passed to the pipeline with `--input`:
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| sample | fastq_1 | fastq_2 | genome |
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| ------ | ------- | ------- | ------ |
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See an example [here](https://github.com/nf-core/test-datasets/blob/methylseq/samplesheet.csv)
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> **Note**: The `genome` column is not yet used but will give the ability to map to multiple genomes in a single run in a future release. See [#181](https://github.com/nf-core/methylseq/issues/181).
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Supplying the reference geneome with `--genome` as before works as usual.
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### Software Updates
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Major updates in commands and software versions for nearly every tool.
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