diff --git a/website/docs/Pipelines/BuildIndices_Pipeline/README.md b/website/docs/Pipelines/BuildIndices_Pipeline/README.md index 547975b821..04b2eea7f0 100644 --- a/website/docs/Pipelines/BuildIndices_Pipeline/README.md +++ b/website/docs/Pipelines/BuildIndices_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/BuildIndices_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [BuildIndices_v3.0.0](https://github.com/broadinstitute/warp/releases) | December, 2023 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | +| [BuildIndices_v4.0.0](https://github.com/broadinstitute/warp/releases) | January, 2025 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![BuildIndices_diagram](./buildindices_diagram.png) @@ -48,6 +48,11 @@ The BuildIndices pipeline can be deployed using [Cromwell](https://cromwell.read The BuildIndices workflow inputs are specified in JSON configuration files. Configuration files for [macaque](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/build_indices/Macaque.json) and [mouse](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/build_indices/Mouse.json) references can be found in the WARP repository. #### Input descriptions +The table below describes the input variables for the BuildIndices workflow. + +:::tip +Marmoset scripts expect a custom-modified input Marmoset GTF file and FASTA file. These inputs and accompanying README are located in a [public Google Drive](https://drive.google.com/drive/folders/15JcUhwOqkJwTVS8BOlA0yIdjh4RwJOdz) maintained by Mike Debardine from the BICAN consortium. +::: | Parameter name | Description | Type | | --- | --- | --- | @@ -64,7 +69,7 @@ The BuildIndices workflow inputs are specified in JSON configuration files. Conf Overall, the BuildIndices workflow: 1. Checks inputs, modifies reference files, and creates STAR index. 2. Calculates chromosome sizes. -3. Builds reference bundle for bwa. +3. Builds reference bundle for bwa-mem2. The tasks and tools used in the BuildIndices workflow are detailed in the table below. @@ -72,7 +77,7 @@ To see specific tool parameters, select the [workflow WDL link](https://github.c | Task name | Tool | Software | Description | | --- | --- | --- | --- | -| BuildStarSingleNucleus | [modify_gtf.py](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/modify_gtf.py), STAR | [warp-tools](https://github.com/broadinstitute/warp-tools/tree/develop), [STAR](https://github.com/alexdobin/STAR) | Checks that the input GTF file contains input genome source, genome build version, and annotation version with correct build source information, modifies files for the STAR aligner, and creates STAR index file. | +| BuildStarSingleNucleus | [modify_gtf.py](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/modify_gtf.py), STAR | [warp-tools](https://github.com/broadinstitute/warp-tools/tree/develop), [STAR](https://github.com/alexdobin/STAR) | Checks that the input GTF file contains input genome source, genome build version, and annotation version with correct build source information, modifies files for the STAR aligner, and creates STAR index file. If "Marmoset" is selected as organism, a [Marmoset-specific custom script](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/modify_gtf_marmoset.py) is run to modify the GTF | | CalculateChromosomeSizes | faidx | [Samtools](http://www.htslib.org/) | Reads the genome FASTA file to create a FASTA index file that contains the genome chromosome sizes. | | BuildBWAreference | index | [bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) | Builds the reference bundle for the bwa aligner. | @@ -84,7 +89,7 @@ The BuildStarSingleNucleus task reads the input GTF file and verifies that the ` **Modify reference files and create STAR index** -The BuildStarSingleNucleus task uses a custom python script, [`modify_gtf.py`](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/modify_gtf.py), and a list of biotypes ([example](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/Biotypes.tsv)) to filter the input GTF file for only the biotypes indicated in the list with the value “Y” in the second column. The defaults in the custom code produce reference outputs that are similar to those built with 10x Genomics reference scripts. +The BuildStarSingleNucleus task uses a custom python script, [`modify_gtf.py`](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/modify_gtf.py) or [`modify_get_marmoset`](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/modify_gtf_marmoset.py), and a list of biotypes ([example](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/Biotypes.tsv)) to filter the input GTF file for only the biotypes indicated in the list with the value “Y” in the second column. The defaults in the custom code produce reference outputs that are similar to those built with 10x Genomics reference scripts. The task uses the filtered GTF file and STAR `--runMode genomeGenerate` to generate the index file for the STAR aligner. Outputs of the task include the modified GTF and compressed STAR index files. @@ -119,10 +124,127 @@ If you use the BuildIndices Pipeline in your research, please consider citing ou Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konwar, K.; Mathews, K.; Palis, K.; Petrillo, N.; Van der Auwera, G.; Wang, C.; Way, J.; Pipelines, W. WDL Analysis Research Pipelines: Cloud-Optimized Workflows for Biological Data Processing and Reproducible Analysis. Preprints 2024, 2024012131. https://doi.org/10.20944/preprints202401.2131.v1 ## Consortia support -This pipeline is supported by the [BRAIN Initiative](https://braininitiative.nih.gov/) (BICCN and BICAN). +This pipeline is supported by the [BRAIN Initiative](https://braininitiative.nih.gov/) (BICCN and BICAN) and SCORCH. If your organization also uses this pipeline, we would like to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). +## Example references +Example references are available in the Broad Public Reference bucket, a Google bucket that hosts reference files at no charge to the end-user. + +### Human +| File Type | File Location | +|-------------------------|--------------| +| Genomics Reference | GRCh38, primary assembly (PRI) | +| Gene annotation (PRI) | GENCODE Release 43 GRCh38.p13 | +| Reference README | `gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/v43_README.txt` | +| STAR Index TAR | `gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_star2.7.10a-Human-GENCODE-build-GRCh38-43.tar` | +| STAR Annotation GTF | `gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf` | +| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/hg38/v0/bwa/v2_2_1/bwa-mem2-2.2.1-Human-GENCODE-build-GRCh38.tar` | +| Chromosome Sizes | `gs://gcp-public-data--broad-references/hg38/v0/bwa/v2_2_1/chrom.sizes` | + +### Mouse + +| File Type | File Location | +|-------------------------|--------------| +| Genomics Reference | GRCm39, primary assembly (PRI) | +| Gene annotation (PRI) | GENCODE Release 32 | +| Reference README | `gs://gcp-public-data--broad-references/GRCm39/star/v2_7_10a/M32_README.txt` | +| STAR Index TAR | `gs://gcp-public-data--broad-references/GRCm39/star/v2_7_10a/modified_star2.7.10a-Mouse-GENCODE-build-GRCm39-M32.tar` | +| STAR Annotation GTF | `gs://gcp-public-data--broad-references/GRCm39/star/v2_7_10a/modified_vM32.annotation.gtf` | +| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/GRCm39/bwa/v2_2_1/bwa-mem2-2.2.1-Mouse-GENCODE-build-GRCm39.tar` | +| Chromosome Sizes | `gs://gcp-public-data--broad-references/GRCm39/bwa/v2_2_1/chrom.sizes` | + +### Macaque +Inputs for the Macaque reference below were modified using a custom tool to handle nuclear mitochondrial inserts, [numty-dumpty](https://github.com/nkschaefer/numty-dumpty). See the README for the [STAR index](https://storage.cloud.google.com/gcp-public-data--broad-references/M.mulatta/Mmul_10/star/v2_7_10a/numty_dumpty/README_STAR.txt) and the [bwa-mem2 index] +(https://storage.cloud.google.com/gcp-public-data--broad-references/M.mulatta/Mmul_10/bwa/v2_2_1/numty_dumpty/README_BWA.txt). + +| File Type | File Location | +|---------------------|--------------| +| Genomics Reference | mmul10 | +| Gene annotation | RefSeq annotation version 103 | +| STAR Index TAR | `gs://gcp-public-data--broad-references/M.mulatta/Mmul_10/star/v2_7_10a/numty_dumpty/numt_modified_star2.7.10a-Macaque-NCBI-build-GCF_003339765.1-103.tar` | +| BWA Index TAR | `gs://gcp-public-data--broad-references/M.mulatta/Mmul_10/bwa/v2_2_1/numty_dumpty/numt_bwa-mem2-2.2.1-Macaque-NCBI-build-GCF_003339765.1.tar` | +| GTF Annotation | `gs://gcp-public-data--broad-references/M.mulatta/Mmul_10/star/v2_7_10a/numty_dumpty/numt_modified_v103.annotation.gtf` | +| Chromosome Sizes | `gs://gcp-public-data--broad-references/M.mulatta/Mmul_10/bwa/v2_2_1/numty_dumpty/numt_chrom.sizes` | + + +This macaque reference works with the Optimus, Multiome, and Paired-tag workflows. However, mitochondrial genes are not demarcated with an "mt-" tag. A separate text file with MT genes is required. An example is the list below: + +``` +ND1 +ND2 +COX1 +COX2 +ATP8 +ATP6 +COX3 +ND3 +ND4L +ND4 +ND5 +ND6 +CYTB +``` + +An example file with this list is located in a public Google bucket here: gs://warp-testing-public/references/BuildIndices_outs/Macaque_MT_genes.txt + +### Marmoset +Marmoset scripts expect a custom-modified input Marmoset GTF file. These inputs and accompanying README are located in a [public Google Drive](https://drive.google.com/drive/folders/15JcUhwOqkJwTVS8BOlA0yIdjh4RwJOdz) maintained by Mike Debardine from the BICAN consortium. + + +| File Type | File Location | +|---------------------|--------------| +| Genomics Reference | mCalJa1.2.pat.X (GenBank Accession GCA_011100555.2 and RefSeq Accession GCF_011100555.1) | +| Gene annotation | Custom (see note above table) | +| Chromosome Sizes | `gs://gcp-public-data--broad-references/mCalJa1/mCalJa1.2.pat.X/chrom.sizes` | +| GTF Annotation | `gs://gcp-public-data--broad-references/mCalJa1/mCalJa1.2.pat.X/modified_vGCF_011100555.1-RS_2023_03.annotation.gtf` | +| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/mCalJa1/mCalJa1.2.pat.X/bwa-mem2-2.2.1-Marmoset-RefSeq-build-mCalJa1.2.pat.X.tar` | +| STAR Index TAR | `gs://gcp-public-data--broad-references/mCalJa1/mCalJa1.2.pat.X/modified_star2.7.10a-Marmoset-RefSeq-build-mCalJa1.2.pat.X-GCF_011100555.1-RS_2023_03.tar` | + +### Armadillo +| File Type | File Location | +|---------------------|--------------| +| Genomic Reference | mDasNov1.hap2 (NCBI) | +| Gene Annotation | RefSeq GCF_030445035.1-RS_2023_07 | +| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/D.novemcinctus/mDasNov1.hap2/cleanome/bwa/v2_2_1/bwa-mem2-2.2.1-Armadillo-NCBI-build-mDasNov1.hap2.tar` | +| Chromosome Sizes | `gs://gcp-public-data--broad-references/D.novemcinctus/mDasNov1.hap2/cleanome/bwa/v2_2_1/chrom.sizes` | +| STAR Index TAR | `gs://gcp-public-data--broad-references/D.novemcinctus/mDasNov1.hap2/cleanome/star/v2_7_10a/modified_star2.7.10a-Armadillo-NCBI-build-mDasNov1.hap2-2.2.tar` | +| GTF Annotation | `gs://gcp-public-data--broad-references/D.novemcinctus/mDasNov1.hap2/cleanome/star/v2_7_10a/modified_v2.2.annotation.gtf` | + +### Opposum + +| File Type | File Location | +|---------------------|--------------| +| Genomic Reference | mMonDom1.pri (NCBI) | +| Gene Annotation | RefSeq GCF_027887165.1-RS_2023_05 (RefSeq link) | +| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/M.domestica/mMonDom1.pri/cleanome/bwa/v2_2_1/bwa-mem2-2.2.1-Opossum-NCBI-build-mMonDom1.pri.tar` | +| Chromosome Sizes | `gs://gcp-public-data--broad-references/M.domestica/mMonDom1.pri/cleanome/bwa/v2_2_1/chrom.sizes` | +| STAR Index TAR | `gs://gcp-public-data--broad-references/M.domestica/mMonDom1.pri/cleanome/star/v2_7_10a/modified_star2.7.10a-Opossum-NCBI-build-mMonDom1.pri-2.2.tar` | +| GTF Annotation | `gs://gcp-public-data--broad-references/M.domestica/mMonDom1.pri/cleanome/star/v2_7_10a/modified_v2.2.annotation.gtf` | + +### Rat + +| File Type | File Location | +|---------------------|--------------| +| Genomic Reference | mRatBN7.2 (NCBI) | +| Gene Annotation | RefSeq GCF_015227675.2-RS_2023_06 | +| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/R.norvegicus/mRatBN7.2/cleanome/bwa/v2_2_1/bwa-mem2-2.2.1-Rat-NCBI-build-mRatBN7.2.tar` | +| Chromosome Sizes | `gs://gcp-public-data--broad-references/R.norvegicus/mRatBN7.2/cleanome/bwa/v2_2_1/chrom.sizes` | +| STAR Index TAR | `gs://gcp-public-data--broad-references/R.norvegicus/mRatBN7.2/cleanome/star/v2_7_10a/modified_star2.7.10a-Rat-NCBI-build-mRatBN7.2-2.2.tar` | +| GTF Annotation | `gs://gcp-public-data--broad-references/R.norvegicus/mRatBN7.2/cleanome/star/v2_7_10a/modified_v2.2.annotation.gtf` | + +### Pig +| File Type | File Location | +|---------------------|--------------| +| Genomic Reference | Sscrofa11.1 (NCBI) | +| Gene Annotation | NCBI Annotation Release 106 (RefSeq GCF_000003025.6_Sscrofa11.1) | +| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/S.scrofa/Sscrofa11.1/cleanome/bwa/v2_2_1/bwa-mem2-2.2.1-Pig-NCBI-build-Sscrofa11.1.tar` | +| Chromosome Sizes | `gs://gcp-public-data--broad-references/S.scrofa/Sscrofa11.1/cleanome/bwa/v2_2_1/chrom.sizes` | +| STAR Index TAR | `gs://gcp-public-data--broad-references/S.scrofa/Sscrofa11.1/cleanome/star/v2_7_10a/modified_star2.7.10a-Pig-NCBI-build-Sscrofa11.1-2.2.tar` | +| GTF Annotation | `gs://gcp-public-data--broad-references/S.scrofa/Sscrofa11.1/cleanome/star/v2_7_10a/modified_v2.2.annotation.gtf` | + + ## Feedback -Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues) for pipeline-related suggestions or questions. \ No newline at end of file +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues) for pipeline-related suggestions or questions. + diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md index 7e91d9f7e9..2952e36c0c 100644 --- a/website/docs/Pipelines/Multiome_Pipeline/README.md +++ b/website/docs/Pipelines/Multiome_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Multiome_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [Multiome v5.9.1](https://github.com/broadinstitute/warp/releases) | November, 2024 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | +| [Multiome v5.9.6](https://github.com/broadinstitute/warp/releases) | January, 2025 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![Multiome_diagram](./multiome_diagram.png) diff --git a/website/docs/Pipelines/Optimus_Pipeline/README.md b/website/docs/Pipelines/Optimus_Pipeline/README.md index 607c2b01a5..a8a3cdd98e 100644 --- a/website/docs/Pipelines/Optimus_Pipeline/README.md +++ b/website/docs/Pipelines/Optimus_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Optimus_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [optimus_v7.8.0](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | October, 2024 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues) | +| [optimus_v7.9.1](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | January, 2025 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues) | ![Optimus_diagram](Optimus_diagram.png) @@ -108,6 +108,7 @@ The example configuration files also contain metadata for the reference files, d | emptydrops_lower | UMI threshold for emptyDrops detection; default is 100. | N/A | | count_exons | Boolean indicating if the workflow should calculate exon counts **when in single-nucleus (sn_rna) mode**. If true, this option will output an additional layer for the h5ad file. By default, it is set to "false". If the parameter is true and used with sc_rnamode, the workflow will return an error. | "true" or "false" (default) | | gex_expected_cells | Optional integer input for the expected number of cells, which is used calculate library-level metrics. The default is set to 3,000. | N/A | +| run_cellbender | Optional boolean used to determine if the Optimus (GEX) pipeline should run CellBender on the output gene expression h5ad file, `h5ad_output_file_gex`; default is "false". | Boolean | #### Pseudogene handling The example Optimus reference files are downloaded directly from GENCODE (see Quickstart table) and are not modified to remove pseudogenes. This is in contrast to the [references created for Cell Ranger](https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/release-notes/references#header) which remove pseudogenes and small RNAs. @@ -148,6 +149,7 @@ To see specific tool parameters, select the task WDL link in the table; then vie | [Metrics.CalculateCellMetrics (alias = CellMetrics)](https://github.com/broadinstitute/warp/blob/master/tasks/skylab/Metrics.wdl) | TagSort | [warp-tools](https://github.com/broadinstitute/warp-tools) | Sorts the BAM file by cell using the cell barcode (CB), molecule barcode (UB) and gene ID (GX) tags and computes cell metrics. | | [RunEmptyDrops.RunEmptyDrops](https://github.com/broadinstitute/warp/blob/master/tasks/skylab/RunEmptyDrops.wdl) | npz2rds.sh, emptyDropsWrapper.R, emptyDrops | [DropletUtils](https://bioconductor.org/packages/release/bioc/html/DropletUtils.html) | Runs custom scripts to convert the NPY and NPZ files to RDS and then uses emptyDrops to identify empty lipid droplets. This step only runs when `counting_mode` = "sc_rna".| | [H5adUtils.OptimusH5adGeneration](https://github.com/broadinstitute/warp/blob/master/tasks/skylab/H5adUtils.wdl) | create_h5ad_optimus.py | Python3 | Merges the gene counts, cell metrics, gene metrics, and emptyDrops data into a h5ad formatted cell-by-gene matrix. The h5ad contains exon counts when using sc_rna mode, and whole-gene counts when running in sn_rna mode. It optionally contains an additional layer for exon counts when running sn_rna mode with `exon_counts` set to true. | +| 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". | More information about the different tags used to flag the data can be found in the [Bam_tags documentation](./Bam_tags.md). @@ -238,8 +240,10 @@ You can determine which type of counts are in the h5ad by looking at the global For sn_rna mode, you can also access whole transcript and exonic counts using AnnData alyers `layers()` method. For example, adata.layers[“exon_counts”]` will return the exonic counts from the output h5ad. +#### 9. Optional: Run CellBender +This task runs when the `run_cellbender` input is set to true. CellBender is a tool for removing background UMIs and thereby helps to flag empty drops. Learn more in the [CellBender documentation](https://cellbender.readthedocs.io/en/latest/). -#### 9. Outputs +#### 10. Outputs Output files of the pipeline include: @@ -269,6 +273,14 @@ The following table lists the output files produced from the pipeline. For sampl | cell_calls | empty_drops_result.csv | emptyDrops results from the RunEmptyDrops task. | CSV | | h5ad_output_file | `.h5ad` | h5ad file with count data (exonic or whole transcript depending on the counting_mode) and metadata. | H5AD | | mtx_files | `.mtx_files.tar` | TAR file with STARsolo matrix market files (barcodes.tsv, features.tsv, and matrix.mtx) | TAR | +| 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. | The h5ad matrix is the default output. This matrix contains the unnormalized (unfiltered), UMI-corrected count matrices, as well as the gene and cell metrics detailed in the [Optimus Count Matrix Overview](./Loom_schema.md). diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md index 3970472fc1..460326d32b 100644 --- a/website/docs/Pipelines/PairedTag_Pipeline/README.md +++ b/website/docs/Pipelines/PairedTag_Pipeline/README.md @@ -6,7 +6,7 @@ slug: /Pipelines/PairedTag_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | |:---:| :---: | :---: | :---: | -| [PairedTag_v1.8.2](https://github.com/broadinstitute/warp/releases) | November, 2024 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | +| [PairedTag_v1.10.0](https://github.com/broadinstitute/warp/releases) | January, 2025 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![pairedtag_diagram](pairedtag_diagram.png) @@ -76,7 +76,7 @@ The Paired-Tag workflow inputs are specified in JSON configuration files. Exampl | star_strand_mode | Optional string for the Optimus (GEX) pipeline for performing STARsolo alignment on forward stranded, reverse stranded, or unstranded data; default is "Forward". | String | | count_exons | Optional boolean for the Optimus (GEX) pipeline indicating if the workflow should calculate exon counts **when in single-nucleus (sn_rna) mode**; if "true" in sc_rna mode, the workflow will return an error; default is "false". | Boolean | | gex_whitelist | Optional file containing the list of valid barcodes for 10x multiome GEX data; default is "gs://gcp-public-data--broad-references/RNA/resources/arc-v1/737K-arc-v1_gex.txt". | File | -| soloMultiMappers | Optional string describing whether or not the Optimus (GEX) pipeline should run STARsolo with the `--soloMultiMappers` flag; default is "Uniform". | String | +| soloMultiMappers | Optional string describing whether or not the Optimus (GEX) pipeline should run STARsolo with the `--soloMultiMappers` flag; default is "EM". | String | | atac_r1_fastq | Array of read 1 paired-end FASTQ files representing a single paired-tag DNA library. | Array[File] | | atac_r2_fastq | Array of barcodes FASTQ files representing a single paired-tag DNA library. | Array[File] | | atac_r3_fastq | Array of read 2 paired-end FASTQ files representing a single paired-tag DNA library. | Array[File] | @@ -120,8 +120,8 @@ The Paired-Tag workflow calls two WARP subworkflows and an additional task which | library_metrics | `_gex__library_metrics.csv` | Optional CSV file containing all library-level metrics calculated with STARsolo for gene expression data. | | atac_library_final | `_atac__library_metrics` | CSV file containing all the library-level metrics calucalted by SnapATAC2. | | cloud_provider | N/A | String describing the cloud provider that should be used to run the workflow; value should be "gcp" or "azure". | -| multimappers_EM_matrix | `UniqueAndMult-EM.mtx` | Optional output produced when `soloMultiMappers` is "EM"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.| -| multimappers_Uniform_matrix | `UniqueAndMult-Uniform.mtx` | Optional output produced when `soloMultiMappers` is "Uniform" (default); see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.| +| multimappers_EM_matrix | `UniqueAndMult-EM.mtx` | Optional output produced when `soloMultiMappers` is "EM" (default); see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.| +| multimappers_Uniform_matrix | `UniqueAndMult-Uniform.mtx` | Optional output produced when `soloMultiMappers` is "Uniform"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.| | multimappers_Rescue_matrix | `UniqueAndMult-Rescue.mtx` | Optional output produced when `soloMultiMappers` is "Rescue"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information. | | multimappers_PropUnique_matrix | `UniqueAndMult-PropUnique.mtx` | Optional output produced when `soloMultiMappers` is "PropUnique"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.|