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|`sample`| The custom sample name. Cannot contain spaces and doesn't have to unique. When the same sample has been given multiple times, the CRAM files will be merged. | string |:heavy_check_mark:|
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|`family`| The family name of the current sample. All samples in the same family will be merged together at the end of the pipeline. Cannot contain spaces | string |:x:|
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|`cram`| Path to the CRAM file to be used by the pipeline for the current sample. | string |:heavy_check_mark:|
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|`crai`| Path to the CRAM index file | string |:x:|
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|`sex`| The sex of the sample to be used by QDNAseq. Sex will be imputed when missing (Options: `male` or `female`) | string |:x:|
|`sample`| The custom sample name. Cannot contain spaces and doesn't have to unique. When the same sample has been given multiple times, the CRAM files will be merged. | string |:heavy_check_mark:|
64
+
|`family`| The family name of the current sample. All samples in the same family will be merged together at the end of the pipeline. Cannot contain spaces | string |:x:|
65
+
|`cram`| Path to the CRAM file to be used by the pipeline for the current sample. | string |:heavy_check_mark:|
66
+
|`crai`| Path to the CRAM index file | string |:x:|
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+
|`sex`| The sex of the sample to be used by QDNAseq. Sex will be imputed when missing (Options: `male` or `female`) | string |:x:|
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See following samplesheet for a working example of a samplesheet (used by the `test` profile of the pipeline):
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