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update docs
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yihming committed Sep 23, 2020
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14 changes: 7 additions & 7 deletions docs/demultiplexing.rst
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Expand Up @@ -173,9 +173,9 @@ demuxEM inputs
- "XIST"
-
* - demuxEM_version
- demuxEM version to use. Currently only support "0.1.4".
- "0.1.4"
- "0.1.4"
- demuxEM version to use. Currently only support "0.1.5".
- "0.1.5"
- "0.1.5"
* - demuxEM_num_cpu
- demuxEM parameter. Number of CPUs to request for demuxEM per pair.
- 8
Expand All @@ -202,17 +202,17 @@ souporcell inputs
- Example
- Default
* - souporcell_version
- souporcell version to use. Available versions: "2020.06", "2020.03".
- "2020.06"
- "2020.06"
- souporcell version to use. Available versions: "2020.07", "2020.03".
- "2020.07"
- "2020.07"
* - souporcell_de_novo_mode
- | souporcell parameter.
| If ``true``, run souporcell in de novo mode without reference genotypes; and if a reference genotype vcf file is provided in the sample sheet, use it **only** for matching the cluster labels computed by souporcell.
| If ``false``, run souporcell with ``--known_genotypes`` option using the reference genotype vcf file specified in sample sheet, and *souporcell_rename_donors* is required in this case.
- true
- true
* - souporcell_num_clusters
- | souporcell parameter. Number of expected clusters when doing clustering.
- | souporcell parameter. Number of expected clusters when doing clustering.
| **This needs to be set when running souporcell.**
- 8
-
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