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doc: add convert input library
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maxibor committed Feb 12, 2024
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Expand Up @@ -25,6 +25,16 @@ AMDirT convert ancientmetagenome-hostassociated_samples_warinnersamplesonly.tsv

where you provide the filtered TSV, which AncientMetagenomeDir samples table the filtered table is derived from,then the output directory where the samplesheets should be saved into, and which tool to generate a samplesheet from.

Alternatively, if you only want specific libraries, and already have pre-filtered the associated AncientMetagenomeDir libraries table, you can also provide it. Here for example:

- the filtered sample table is : `ancientmetagenome-hostassociated_samples_warinnersamplesonly.tsv`
- the matching filtered libraries table is: `ancientmetagenome-hostassociated_libraries_warinnerlibrariesonly.tsv`

```bash
mkdir -p samplesheets/
AMDirT convert --libraries ancientmetagenome-hostassociated_libraries_warinnerlibrariesonly.tsv ancientmetagenome-hostassociated_samples_warinnersamplesonly.tsv ancientmetagenome-hostassociated -o samplesheets/ --<tool>
```

See [Output](#output) for descriptions of all output files.

> ⚠️ _When using a **pipeline input samplesheet**, you should always double check the sheet is correctly configured. We cannot guarantee accuracy between metadata and sequencing files._
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