From 869cade1a791baaeb8ef675bdf271111e6ebe3f0 Mon Sep 17 00:00:00 2001 From: ekiernan Date: Thu, 7 Sep 2023 12:02:35 -0400 Subject: [PATCH] Updated Multiome version and link to biotypes TSV --- website/docs/Pipelines/Multiome_Pipeline/README.md | 2 +- website/docs/Pipelines/SlideSeq_Pipeline/README.md | 2 +- .../Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md index 859b32ee23..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) | September, 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) 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.