Update infercnv_status docs

docs/merged_objects.md

@@ -195,7 +195,7 @@ Each such list will contain the following fields:
 | `infercnv_reference_celltypes` | Vector of consensus cell type labels which would be specified for the normal reference cells in `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample was obtained from normal or non-cancerous tissue this will not be present                                                                                                                                                   |
 | `infercnv_num_reference_cells` | The total number of normal reference cells included in the `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample was obtained from normal or non-cancerous tissue this will be `NA` | 
 | `infercnv_diagnosis_groups` | The broad diagnosis group used to determine which cell types should be considered as part of the normal cell reference for `inferCNV`. If this value is `Non-cancerous`, `inferCNV` was not run | 
-| `infercnv_success`             | Boolean indicating if `inferCNV` succeeded. `TRUE` indicates that `inferCNV` successfully ran, `FALSE` indicates that `inferCNV` was attempted but failed during inference for an unknown reason, and `NA` indicates that `inferCNV` was not run due to insufficient normal reference cells. Only present when CNV inference was attempted                                         |
+| `infercnv_status`             | String indicating the status of running `inferCNV`. A value of "success" indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells, and "skipped_non_cancerous" indicates that `inferCNV` was not run because the sample was non-cancerous. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted                                         |
 | `infercnv_options`             | A list containing the contents of the `objects` slot from the [final `inferCNV` results object](https://github.com/broadinstitute/infercnv/wiki/Output-Files#infercnv-object-files) containing all parameters specified used when running `inferCNV`. Only present when CNV inference was performed                                                                                |
 | `infercnv_table`               | The `inferCNV` metadata table with detailed CNV results output from `inferCNV`. This data frame corresponds to the [`map_metadata_from_infercnv.txt` table calculated from the HMM results](https://github.com/broadinstitute/infercnv/wiki/Extracting-features). Only present when CNV inference was performed                                                                       |
 

docs/sce_file_contents.md

@@ -190,7 +190,7 @@ metadata(sce) # experiment metadata
 | `infercnv_reference_celltypes` | Vector of consensus cell type labels which would be specified for the normal reference cells in `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample is obtained from normal or non-cancerous tissue this will not be present                                                                                                                                                   |
 | `infercnv_num_reference_cells` | The total number of normal reference cells included in the `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample is obtained from normal or non-cancerous tissue this will be `NA` | 
 | `infercnv_diagnosis_groups` | The broad diagnosis group used to determine which cell types should be considered as part of the normal cell reference for `inferCNV`. If this value is `Non-cancerous`, `inferCNV` was not run | 
-| `infercnv_success`             | Boolean indicating if `inferCNV` succeeded. `TRUE` indicates that `inferCNV` successfully ran, `FALSE` indicates that `inferCNV` was attempted but failed during inference for an unknown reason, and `NA` indicates that `inferCNV` was not run due to insufficient normal reference cells. Only present when CNV inference was attempted                                         |
+| `infercnv_status`             | String indicating the status of running `inferCNV`. A value of "success" indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells, and "skipped_non_cancerous" indicates that `inferCNV` was not run because the sample was non-cancerous. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted                                         |
 | `infercnv_options`             | A list containing the contents of the `objects` slot from the [final `inferCNV` results object](https://github.com/broadinstitute/infercnv/wiki/Output-Files#infercnv-object-files) containing all parameters specified used when running `inferCNV`. Only present when CNV inference was performed                                                                                |
 | `infercnv_table`               | The `inferCNV` metadata table with detailed CNV results output from `inferCNV`. This data frame corresponds to the [`map_metadata_from_infercnv.txt` table calculated from the HMM results](https://github.com/broadinstitute/infercnv/wiki/Extracting-features). Only present when CNV inference was performed                                                                       |