Re-build human genome annotations with GDC fasta

[kelly-sovacool]

Changes

• Rebuilt hg19 and hg38 annotations with the GDC reference fasta, which includes additional sequences. These are stored in a shared location for use in other pipelines too: /data/CCBR_Pipeliner/db/PipeDB/GDC_refs/
• Copied files to FRCE: /mnt/projects/CCBR-Pipelines/db/GDC_refs

See the snakemake workflow here for how these were built: https://github.com/CCBR/build-renee-refs

Issues

• Resolves Change human reference fasta  #129
• Resolves change fasta for hg19 #138
• Resolves set default human genome+annotation combo to match GDC #128

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• Update docs if there are any API changes.
• 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/

[kelly-sovacool]

Running tests.

RENEE_REPO=/data/CCBR_Pipeliner/Pipelines/RENEE/renee-dev-sovacool
for genome in $(ls $RENEE_REPO/config/genomes/biowulf/ | grep hg |  sed 's/.json//'); do
    $RENEE_REPO/bin/renee run \
        --input $RENEE_REPO/.tests/*.R1.fastq.gz \
        --genome $genome \
        --mode slurm \
        --output /data/$USER/renee_test_$genome \
        --sif-cache /data/CCBR_Pipeliner/SIFS \
        &> /data/$USER/renee_shell.${genome}.out
done

Job status

generate table

cd /data/sovacoolkl/
for f in $(ls | grep renee_shell); do genome=$(echo $f |  sed 's/renee_shell\.//' | sed 's/\.out//'); jobid=$(grep master $f | sed 's/.*: //'); echo "| $genome | $jobid |  |"; done

genome	slurm id	status
hg19_19	31994530	RUNNING
hg19_36lift37	31994535	RUNNING
hg38_30	31994547	RUNNING
hg38_34	31994560	RUNNING
hg38_36	31994162	RUNNING
hg38_38	31994566	RUNNING
hg38_41	31994570	RUNNING
hg38_45	31994583	RUNNING

Update

All pipeline runs completed successfully. Jobby initially failed because it wasn't in my path when I submitted these, but after running jobby manually I verified that all jobs completed successfully.

[kopardev]

Please see comments before merging.

[kelly-sovacool]

@kopardev this is ready for your re-review