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feat: add hg38 v45 reference genome #127

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May 21, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
## RENEE development version

- Support hg38 release 45 on biowulf & FRCE. (#127, @kelly-sovacool)
- Show the name of the pipeline rather than the python script for CLI help messages. (#131, @kelly-sovacool)

## RENEE 2.5.12
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25 changes: 25 additions & 0 deletions config/genomes/biowulf/hg38_45.json
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{
"references": {
"rnaseq": {
"GENOMEFILE": "/data/CCBR_Pipeliner/Pipelines/RENEE/resources/fastas/GRCh38.primary_assembly.genome.fa",
"GENOME": "/data/CCBR_Pipeliner/Pipelines/RENEE/resources/fastas/GRCh38.primary_assembly.genome.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/gencode.v45.primary_assembly.annotation.gtf",
"GENOME_STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/STAR/2.7.6a/genome",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/annotate.genes.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/annotate.isoforms.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/refFlat.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/genes.ref.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/geneinfo.bed",
"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/qualimap_info.txt",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/karyobeds/",
"KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/karyoplot_gene_coordinates.txt",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/rsemref/hg38_45",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/hg38_45.rRNA_interval_list",
"ORGANISM": "hg38",
"TINREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45/transcripts.protein_coding_only.bed12",
"FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_hg38_GRCh38_v2.0.0.tsv.gz",
"FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_hg38_GRCh38_v2.0.0.tsv",
"FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
}
}
}
25 changes: 25 additions & 0 deletions config/genomes/frce/hg38_45.json
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{
"references": {
"rnaseq": {
"GENOMEFILE": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/GRCh38.primary_assembly.genome.fa",
"GENOME": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/GRCh38.primary_assembly.genome.fa",
"GTFFILE": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/gencode.v45.primary_assembly.annotation.gtf",
"GENOME_STARDIR": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/STAR/2.7.6a/genome",
"ANNOTATE": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/annotate.genes.txt",
"ANNOTATEISOFORMS": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/annotate.isoforms.txt",
"REFFLAT": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/refFlat.txt",
"BEDREF": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/genes.ref.bed",
"GENEINFO": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/geneinfo.bed",
"QUALIMAP_INFO": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/qualimap_info.txt",
"KARYOBEDS": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/karyobeds/",
"KARYOPLOTER": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/karyoplot_gene_coordinates.txt",
"RSEMREF": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/rsemref/hg38_45",
"RRNALIST": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/hg38_45.rRNA_interval_list",
"ORGANISM": "hg38",
"TINREF": "/mnt/projects/CCBR-Pipelines/genomes/hg38_45/transcripts.protein_coding_only.bed12",
"FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_hg38_GRCh38_v2.0.0.tsv.gz",
"FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_hg38_GRCh38_v2.0.0.tsv",
"FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
}
}
}
2 changes: 1 addition & 1 deletion config/templates/tools.json
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Expand Up @@ -32,7 +32,7 @@
"FASTAWITHADAPTERSETD": "resources/TruSeq_and_nextera_adapters.consolidated.fa",
"FASTQ_SCREEN_CONFIG": "resources/fastq_screen.conf",
"FASTQ_SCREEN_CONFIG2": "resources/fastq_screen_2.conf",
"KRAKENBACDB": "/data/CCBR_Pipeliner/Pipelines/RENEE/resources/shared_resources/20180907_standard_kraken2",
"KRAKENBACDB": "shared_resources/20180907_standard_kraken2",
"Trimsettings": "---------------------------- TRIMMOMATIC parameters ----------------------------------------------------------",
"LEADINGQUALITY": 10,
"TRAILINGQUALITY": 10,
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1 change: 1 addition & 0 deletions docs/RNA-seq/Resources.md
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Expand Up @@ -14,6 +14,7 @@ Bundled Biowulf Reference Genomes
| hg38_34 | Homo sapiens (human) | [Gencode Release v34](https://www.gencodegenes.org/human/release_34.html) | [GRCh38](https://www.gencodegenes.org/human/release_34.html), Annotation Release date: 04/2020 |
| hg38_38 | Homo sapiens (human) | [Gencode Release v38](https://www.gencodegenes.org/human/release_38.html) | [GRCh38](https://www.gencodegenes.org/human/release_38.html), Annotation Release date: 05/2021 |
| hg38_41 | Homo sapiens (human) | [Gencode Release v41](https://www.gencodegenes.org/human/release_41.html) | [GRCh38](https://www.gencodegenes.org/human/release_41.html), Annotation Release date: 07/2022 |
| hg38_45 | Homo sapiens (human) | [Gencode Release v45](https://www.gencodegenes.org/human/release_45.html) | [GRCh38](https://www.gencodegenes.org/human/release_45.html), Annotation Release date: 03/2023 |
| mm10_M21 | Mus musculus (mouse) | [Gencode Release M21](https://www.gencodegenes.org/mouse/release_M21.html) | [GRCm38](https://www.gencodegenes.org/mouse/release_M21.html), Annotation Release date: 04/2019 |
| mm10_M23 | Mus musculus (mouse) | [Gencode Release M23](https://www.gencodegenes.org/mouse/release_M23.html) | [GRCm38](https://www.gencodegenes.org/mouse/release_M23.html), Annotation Release date: 09/2019 |
| mm10_M25 | Mus musculus (mouse) | [Gencode Release M25](https://www.gencodegenes.org/mouse/release_M25.html) | [GRCm38](https://www.gencodegenes.org/mouse/release_M25.html), Annotation Release date: 04/2020 |
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