Np add fasta files to buildind docs (#1791)

* dummy commit

* doc changes

* doc changes

* Update website/docs/Pipelines/BuildIndices_Pipeline/README.md

Co-authored-by: Elizabeth Kiernan <55763654+ekiernan@users.noreply.github.com>

* Update website/docs/Pipelines/BuildIndices_Pipeline/README.md

Co-authored-by: Elizabeth Kiernan <55763654+ekiernan@users.noreply.github.com>

* Update website/docs/Pipelines/BuildIndices_Pipeline/README.md

Co-authored-by: Jessica Way <jway@broadinstitute.org>

---------

Co-authored-by: Elizabeth Kiernan <55763654+ekiernan@users.noreply.github.com>
Co-authored-by: Jessica Way <jway@broadinstitute.org>

Author: 3 people

website/docs/Pipelines/BuildIndices_Pipeline/README.md

@@ -146,6 +146,7 @@ Example references are available in the Broad Public Reference bucket, a Google
 | 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` |
+| FASTA                  | `gs://gcp-public-data--broad-references/hg38/v0/single_nucleus_smart_seq_2/GRCh38.primary_assembly.genome.fa` |
 
 
 ### Mouse
@@ -159,6 +160,8 @@ Example references are available in the Broad Public Reference bucket, a Google
 | 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` |
+| FASTA                  | `gs://gcp-public-data--broad-references/GRCm39/single_nucleus_smart_seq_2/GRCm39.primary_assembly.genome.fa` |
+
 
 ### 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]
@@ -172,6 +175,8 @@ Inputs for the Macaque reference below were modified using a custom tool to hand
 | BWA Index TAR      | `gs://gcp-public-data--broad-references/M.mulatta/Mmul_10/bwa/v2_2_1/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/10x_filtered/mt_v103_modified.annotation.gtf` |
 | Chromosome Sizes   | `gs://gcp-public-data--broad-references/M.mulatta/Mmul_10/bwa/v2_2_1/chrom.sizes` |
+| FASTA              | `gs://gcp-public-data--broad-references/M.mulatta/Mmul_10/single_nucleus_smart_seq_2/GCF_003339765.1_Mmul_10_genomic.fna` |
+
 
 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: