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|`sample`| Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
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|`fastq_1`| Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz". |
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|`fastq_2`| Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz". |
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|`fastq_1`| Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz". |
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|`fastq_2`| Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz". |
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An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
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