| | 1 | = Updating to Reggie 4.26 = |
| | 2 | |
| | 3 | == A. Before updating Reggie == |
| | 4 | |
| | 5 | === 1. Install a new Picard version on the prime cluster === |
| | 6 | |
| | 7 | We need Picard version 2.22.3 or higher since it fixes a problem with !NovaSeq data files and the !CheckIlluminaDirectory |
| | 8 | function. Verify that the `<picard><path>` setting `reggie-config.xml` is poiting to the correct installation directory |
| | 9 | and modify if needed. Picard can be downloaded from https://github.com/broadinstitute/picard/releases. |
| | 10 | |
| | 11 | == B. Update Reggie == |
| | 12 | |
| | 13 | Update Reggie to version 4.26 as usual. Do not forget to run the Installation wizard. |
| | 14 | |
| | 15 | == C. After updating Reggie == |
| | 16 | |
| | 17 | === 1. Upload CTG sample sheet template === |
| | 18 | |
| | 19 | Upload the `CTG_SampleSheet.xlsx` file to the `/home/SCANB/Templates` directory in BASE. |
| | 20 | |
| | 21 | === 2. Import variant annotations === |
| | 22 | |
| | 23 | In the **RNA library preparation and analysis**/**Variant calling pipeline** section, |
| | 24 | run the **Import variants for existing variant call raw bioassays** wizard. This wizard |
| | 25 | will import variants that are found in some interesting genes as annotations to existing |
| | 26 | raw bioassay items and will take several minutes to run. The same functionality is |
| | 27 | included in the regular variant calling script so the wizard is not needed in the future. |
| | 28 | See #1229 for more information. |
| | 29 | |
| | 30 | |
| | 31 | |
| | 32 | |
