diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md index f11e92137b..ef3c77cf54 100644 --- a/pipelines/skylab/multiome/Multiome.changelog.md +++ b/pipelines/skylab/multiome/Multiome.changelog.md @@ -1,7 +1,7 @@ # 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) diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md index 0efc2ab86b..c32b6a3bc0 100644 --- a/website/docs/Pipelines/Multiome_Pipeline/README.md +++ b/website/docs/Pipelines/Multiome_Pipeline/README.md @@ -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 @@ -114,14 +114,14 @@ The Multiome workflow calls two WARP subworkflows, one external subworkflow (opt | gene_metrics_gex | `_gex.gene_metrics.csv.gz` | CSV file containing the per-gene metrics. | | cell_calls_gex | `_gex.emptyDrops` | TSV file containing the EmptyDrops results when the Optimus workflow is run in sc_rna mode. | | h5ad_output_file_gex | `_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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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 | `` | 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. |