feat: add hg38 v45 reference genome

[kelly-sovacool]

Changes

Adds configuration files for gencode release 45 of hg38.

Steps

Using PRI regions

• source: https://www.gencodegenes.org/human/
• gtf: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/gencode.v45.primary_assembly.annotation.gtf.gz
• fasta: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/GRCh38.primary_assembly.genome.fa.gz

build command

renee build \
    --sif-cache /data/CCBR_Pipeliner/SIFS \
    --ref-fa GRCh38.primary_assembly.genome.fa \
    --ref-name hg38 \
    --ref-gtf gencode.v45.primary_assembly.annotation.gtf \
    --gtf-ver 45 \
    --output /data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45

change ownership

chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45
chmod -R a+rX /data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_45

testing

biowulf ✅

/data/CCBR_Pipeliner/Pipelines/RENEE/renee-dev-sovacool/bin/renee run \
    --input /data/CCBR_Pipeliner/Pipelines/RENEE/develop/.tests/*.R1.fastq.gz \
    --genome hg38_45 \
    --mode slurm \
    --output /data/$USER/renee_test_gencode-45 \
    --sif-cache /data/CCBR_Pipeliner/SIFS

frce [in progress]

/mnt/projects/CCBR-Pipelines/pipelines/RENEE/renee-dev-sovacool/bin/renee run \
    --input latest/.tests/*.R?.fastq.gz \
    --output /scratch/cluster_scratch/$USER/renee_test_gencode-45 \
    --genome hg38_45 \
    --mode slurm \
    --tmp-dir /scratch/cluster_scratch/$USER \
    --sif-cache /mnt/projects/CCBR-Pipelines/SIFs

Issues

Resolves #126

PR Checklist

(~Strikethrough~ any points that are not applicable.)

• [x] This comment contains a description of changes with justifications, with any relevant issues linked.
• [x] Update docs if there are any API changes.
• [x] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[kopardev]

Is fasta different from the one in /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/fastas ?

[kelly-sovacool]

Is fasta different from the one in /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/fastas ?

I had assumed they would be different, but they are actually the same. I'll switch it to use the existing one.

[kelly-sovacool]

this is ready @kopardev