Updated Multiome version and link to biotypes TSV

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:[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)
 

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
 

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.