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Update Multiome.changelog.md for Cell Bender (broadinstitute#1149)
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aawdeh authored Dec 13, 2023
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4 changes: 2 additions & 2 deletions pipelines/skylab/multiome/Multiome.changelog.md
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# 3.0.1
2023-12-08 (Date of Last Commit)

2023-12-12 (Date of Last Commit)
* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
* Downgraded Cell Bender from v0.3.1 to v0.3.0

# 3.0.0
2023-11-22 (Date of Last Commit)
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18 changes: 9 additions & 9 deletions website/docs/Pipelines/Multiome_Pipeline/README.md
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Expand Up @@ -94,7 +94,7 @@ The Multiome workflow calls two WARP subworkflows, one external subworkflow (opt
| ATAC ([WDL](https://github.com/broadinstitute/warp/blob/develop/pipelines/skylab/multiome/atac.wdl) and [documentation](../ATAC/README)) | fastqprocess, bwa-mem, SnapATAC2 | Workflow used to analyze 10x single-cell ATAC data. |
| Optimus ([WDL](https://github.com/broadinstitute/warp/blob/develop/pipelines/skylab/optimus/Optimus.wdl) and [documentation](../Optimus_Pipeline/README)) | fastqprocess, STARsolo, Emptydrops | Workflow used to analyze 10x single-cell GEX data. |
| JoinMultiomeBarcodes as JoinBarcodes ([WDL](https://github.com/broadinstitute/warp/blob/develop/tasks/skylab/H5adUtils.wdl)) | Python3 | Task that adds an extra column to the Optimus metrics `h5ad.obs` property that lists the respective ATAC barcodes for each gene expression barcode. It also adds an extra column to the ATAC metrics `h5ad.obs` property to link ATAC barcodes to gene expression barcodes. |
| CellBender.run_cellbender_remove_background_gpu as CellBender ([WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.1/wdl/cellbender_remove_background.wdl))| CellBender | Optional task that runs the `cellbender_remove_background.wdl` WDL script directly from the [CellBender GitHub repository](https://github.com/broadinstitute/CellBender/tree/master), depending on whether the input `run_cellbender` is "true" or "false". |
| CellBender.run_cellbender_remove_background_gpu as CellBender ([WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.0/wdl/cellbender_remove_background.wdl))| CellBender | Optional task that runs the `cellbender_remove_background.wdl` WDL script directly from the [CellBender GitHub repository](https://github.com/broadinstitute/CellBender/tree/master), depending on whether the input `run_cellbender` is "true" or "false". |

## Outputs

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| gene_metrics_gex | `<input_id>_gex.gene_metrics.csv.gz` | CSV file containing the per-gene metrics. |
| cell_calls_gex | `<input_id>_gex.emptyDrops` | TSV file containing the EmptyDrops results when the Optimus workflow is run in sc_rna mode. |
| h5ad_output_file_gex | `<input_id>_gex.h5ad` | h5ad (Anndata) file containing the raw cell-by-gene count matrix, gene metrics, cell metrics, and global attributes. Also contains equivalent ATAC barcode for each gene expression barcode in the `atac_barcodes` column of the `h5ad.obs` property. See the [Optimus Count Matrix Overview](../Optimus_Pipeline/Loom_schema.md) for more details. |
| cell_barcodes_csv | `<cell_csv>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.1/wdl/cellbender_remove_background.wdl) for more information. |
| checkpoint_file | `<ckpt_file>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.1/wdl/cellbender_remove_background.wdl) for more information. |
| h5_array | `<h5_array>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.1/wdl/cellbender_remove_background.wdl) for more information. |
| html_report_array | `<report_array>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.1/wdl/cellbender_remove_background.wdl) for more information. |
| log | `<log>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.1/wdl/cellbender_remove_background.wdl) for more information. |
| metrics_csv_array | `<metrics_array>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.1/wdl/cellbender_remove_background.wdl) for more information. |
| output_directory | `<output_dir>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.1/wdl/cellbender_remove_background.wdl) for more information. |
| summary_pdf | `<pdf>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [WDL](https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.1/wdl/cellbender_remove_background.wdl) for more information. |
| cell_barcodes_csv | `<cell_csv>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |
| checkpoint_file | `<ckpt_file>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |
| h5_array | `<h5_array>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |
| html_report_array | `<report_array>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |
| log | `<log>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |
| metrics_csv_array | `<metrics_array>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |
| output_directory | `<output_dir>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |
| summary_pdf | `<pdf>` | Optional output produced when `run_cellbender` is "true"; see CellBender [documentation](https://cellbender.readthedocs.io/en/latest/usage/index.html) and [GitHub repository](https://github.com/broadinstitute/CellBender/tree/master) for more information. |



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