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Update Multiome.changelog.md for Cell Bender #1149

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Dec 13, 2023
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Update Multiome.changelog.md for Cell Bender #1149

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abcb910
Update Multiome.changelog.md for Cell Bender
aawdeh Dec 12, 2023
08e9086
Update pipeline version in Multiome.wdl
aawdeh Dec 12, 2023
b4230a6
update multiome readme
kayleemathews Dec 13, 2023
6b95397
Update Multiome.changelog.md
aawdeh Dec 13, 2023
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change pipeline version
aawdeh Dec 13, 2023
b28e53d
Changed pipeline version back to 3.0.1 in Multiome.wdl
aawdeh Dec 13, 2023
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Merge branch 'develop' into aa-updatemultiomechangelog
aawdeh 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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