From aced1bf8a9b1cc6dd77d503e16f23fa814e30bda Mon Sep 17 00:00:00 2001 From: Kaylee Mathews <95316074+kayleemathews@users.noreply.github.com> Date: Fri, 8 Sep 2023 10:31:25 -0400 Subject: [PATCH] KM Add multiome RRID (#1074) * add rrid * Update README.md * Updated Multiome version and link to biotypes TSV --------- Co-authored-by: ekiernan Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> --- website/docs/Pipelines/Multiome_Pipeline/README.md | 6 +++++- website/docs/Pipelines/SlideSeq_Pipeline/README.md | 2 +- .../README.md | 2 +- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md index 82fcabd92e..39fa6704f7 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 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:warp-pipelines-help@broadinstitute.org) | +| [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:warp-pipelines-help@broadinstitute.org) | ![Multiome_diagram](./multiome_diagram.png) @@ -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). diff --git a/website/docs/Pipelines/SlideSeq_Pipeline/README.md b/website/docs/Pipelines/SlideSeq_Pipeline/README.md index 5f6b3ed084..a7ee939195 100644 --- a/website/docs/Pipelines/SlideSeq_Pipeline/README.md +++ b/website/docs/Pipelines/SlideSeq_Pipeline/README.md @@ -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 diff --git a/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md b/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md index 7df21ae4bb..ecc3503e20 100644 --- a/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md +++ b/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md @@ -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.