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KM Add multiome RRID #1074

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6 changes: 5 additions & 1 deletion website/docs/Pipelines/Multiome_Pipeline/README.md
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Expand Up @@ -7,7 +7,7 @@ slug: /Pipelines/Multiome_Pipeline/README

| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
| :----: | :---: | :----: | :--------------: |
| [Multiome v1.0.0](https://github.com/broadinstitute/warp/releases) | June, 2023 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:[email protected]) |
| [Multiome v2.0.0](https://github.com/broadinstitute/warp/releases) | September, 2023 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:[email protected]) |

![Multiome_diagram](./multiome_diagram.png)

Expand Down Expand Up @@ -111,6 +111,10 @@ The Multiome workflow calls two subworkflows, which are described briefly in the

All Multiome pipeline releases are documented in the [Multiome changelog](https://github.com/broadinstitute/warp/blob/develop/pipelines/skylab/multiome/Multiome.changelog.md) and tested using [plumbing and scientific test data](https://github.com/broadinstitute/warp/blob/develop/pipelines/skylab/multiome/test_inputs/test_data_overview.md). To learn more about WARP pipeline testing, see [Testing Pipelines](https://broadinstitute.github.io/warp/docs/About_WARP/TestingPipelines).

## Citing the Multiome Pipeline
Please identify the pipeline in your methods section using the Multiome Pipeline's [SciCrunch resource identifier](https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_024217/resolver?q=SCR_024217&l=SCR_024217&i=rrid:scr_024217).
* Ex: *Multiome Pipeline (RRID:SCR_024217)*

## Consortia support
This pipeline is supported by the [BRAIN Initiative](https://braininitiative.nih.gov/) (BICCN and BICAN).

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2 changes: 1 addition & 1 deletion website/docs/Pipelines/SlideSeq_Pipeline/README.md
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Expand Up @@ -72,7 +72,7 @@ The Slide-seq workflow inputs are specified in JSON configuration files. Example

#### Pseudogene handling

The example Slide-seq reference files are created using the [BuildIndices pipeline](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/build_indices/BuildIndices.wdl). The BuildIndices pipeline modifies a given GTF downloaded from GENCODE to only include biotypes that are listed in a tab separated file ([biotypes.tsv](https://github.com/broadinstitute/warp/blob/master/dockers/skylab/snss2-build-indices/Biotypes.tsv)). The example references do not include the pseudogene biotype. Learn more about Ensembl biotypes in the [Ensembl overview](https://m.ensembl.org/info/genome/genebuild/biotypes.html).
The example Slide-seq reference files are created using the [BuildIndices pipeline](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/build_indices/BuildIndices.wdl). The BuildIndices pipeline modifies a given GTF downloaded from GENCODE to only include biotypes that are listed in a tab separated file ([biotypes.tsv](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/Biotypes.tsv)). The example references do not include the pseudogene biotype. Learn more about Ensembl biotypes in the [Ensembl overview](https://m.ensembl.org/info/genome/genebuild/biotypes.html).

#### Sample inputs for analyses in a Terra Workspace

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Expand Up @@ -59,7 +59,7 @@ There is an [example configuration (JSON) file](https://github.com/broadinstitut
The table below details the Multi-snSS2 inputs. The pipeline is designed to take in an array of paired-end reads in the form of two FASTQ files per cell.

* The example mouse reference inputs are created using the [BuildIndices Pipeline](https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/build_indices).
* The pipeline modifies a given GTF downloaded from GENCODE to only include biotypes that are listed in a tab separated file ([biotypes.tsv](https://github.com/broadinstitute/warp/blob/develop/dockers/skylab/build-indices/Biotypes.tsv)).
* The pipeline modifies a given GTF downloaded from GENCODE to only include biotypes that are listed in a tab separated file ([biotypes.tsv](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/build-indices/Biotypes.tsv)).
* The example references do not include the pseudogene biotype. Learn more about Ensembl biotypes in the [Ensembl overview](https://m.ensembl.org/info/genome/genebuild/biotypes.html).
* To enable intron counting, the workflow calls a [python script](https://github.com/broadinstitute/warp/blob/develop/dockers/skylab/build-indices/add-introns-to-gtf.py) to create a custom GTF with intron annotations. Introns are considered any part of a contig that is not exonic nor intergenic.

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