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Re-build human genome annotations with GDC fasta #136

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merged 26 commits into from
Aug 27, 2024
Merged

Re-build human genome annotations with GDC fasta #136

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7efdf04
feat: update indices with GDC fasta including viruses & decoys
kelly-sovacool Jun 21, 2024
7dfd23b
feat: copied new hg38 indices to FRCE
kelly-sovacool Jun 21, 2024
8ff018a
chore: update changelog
kelly-sovacool Jun 21, 2024
a721d3e
docs: note hg38 uses the GDC fasta
kelly-sovacool Jun 24, 2024
1b5ff5f
feat: add rebuilt hg19 19 & 36-lift-37 genomes
kelly-sovacool Aug 1, 2024
593b262
docs: add new hg19/38 builds
kelly-sovacool Aug 1, 2024
70ee7ad
feat: set hg38_36 as the default genome
kelly-sovacool Aug 1, 2024
d4fa888
chore: update changelog
kelly-sovacool Aug 1, 2024
b8013fb
docs: set --genome example to hg38_36
kelly-sovacool Aug 1, 2024
af9ca32
Merge branch 'main' into iss-129
kelly-sovacool Aug 2, 2024
a4b12fb
test: setup basic igenomes config for testing purposes
kelly-sovacool Aug 2, 2024
c27b00a
Merge branch 'main' into iss-129
kelly-sovacool Aug 2, 2024
fa4d6c7
Merge branch 'main' into iss-129
kelly-sovacool Aug 2, 2024
df33cba
Merge branch 'main' into iss-129
kelly-sovacool Aug 5, 2024
086b6ab
docs: rename hg19_36lift37 to hg19_36 for simplicity
kelly-sovacool Aug 5, 2024
b887a23
docs: link to build-renee-refs repo
kelly-sovacool Aug 5, 2024
5e19438
docs: note how hg19+virus+decoy fasta created
kelly-sovacool Aug 5, 2024
dc88c7a
test: make sure error is thrown if genome config not found
kelly-sovacool Aug 5, 2024
098befc
test: update tests with new default genome behavior
kelly-sovacool Aug 5, 2024
b5cb2f6
chore: Merge branch 'main' into iss-129
kelly-sovacool Aug 5, 2024
f063f82
docs: remove errant "hg38_v36" -- remove v
kelly-sovacool Aug 5, 2024
e025aff
chore: Merge branch 'main' into iss-129
kelly-sovacool Aug 13, 2024
4c9a522
refactor: simplify genome picking based on hpc & --genome arg
kelly-sovacool Aug 13, 2024
39f7479
test: use main.py instead of bin/renee in tests
kelly-sovacool Aug 13, 2024
5016474
test: fix test string
kelly-sovacool Aug 13, 2024
a7d6ebc
Merge branch 'main' into iss-129
kelly-sovacool Aug 26, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,8 @@
### New features

- Support hg38 release 45 on biowulf & FRCE. (#127, @kelly-sovacool)
- hg38 genome index files now include decoy & virus sequences. (#136, @kelly-sovacool)
- Additionally, `--genome` is no longer required and is set to `hg38_36` by default.
- Set default shared singularity SIF directory for biowulf and frce. (#94, @kelly-sovacool)
- Add `renee gui` subcommand to launch the graphical user interface. (#94, @kelly-sovacool)
- Previously, `renee_gui` (with an underscore) was a command in the `ccbrpipeliner` module.
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -111,7 +111,7 @@ renee run --help
# Grab an interactive node
sinteractive --mem=110g --cpus-per-task=12 --gres=lscratch:200
module load ccbrpipeliner
renee run --input .tests/*.R?.fastq.gz --output /data/$USER/RNA_hg38 --genome hg38_30 --mode local
renee run --input .tests/*.R?.fastq.gz --output /data/$USER/RNA_hg38 --genome hg38_36 --mode local

# @slurm: uses slurm and singularity execution method
# The slurm MODE will submit jobs to the cluster.
Expand All @@ -121,7 +121,7 @@ module load ccbrpipeliner
renee run \
--input .tests/*.R?.fastq.gz \
--output /data/$USER/RNA_hg38 \
--genome hg38_30 \
--genome hg38_36 \
--mode slurm \
--sif-cache /data/CCBR_Pipeliner/SIFS
```
Expand All @@ -146,7 +146,7 @@ with the following values:
renee run \
--input .tests/*.R?.fastq.gz \
--output /scratch/cluster_scratch/$USER/RNA_hg38 \
--genome hg38_30 \
--genome hg38_36 \
--mode slurm \
--tmp-dir /scratch/cluster_scratch/$USER \
--sif-cache /mnt/projects/CCBR-Pipelines/SIFs
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30 changes: 15 additions & 15 deletions config/genomes/biowulf/hg19_19.json
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@@ -1,22 +1,22 @@
{
"references": {
"rnaseq": {
"GENOMEFILE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/hg19.fa",
"GENOME": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/hg19.fa",
"GTFFILE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/19.gtf",
"GENOME_STARDIR": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/STAR/2.7.6a/genome",
"ANNOTATE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/annotate.genes.txt",
"ANNOTATEISOFORMS": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/annotate.isoforms.txt",
"REFFLAT": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/refFlat.txt",
"BEDREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/genes.ref.bed",
"GENEINFO": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/geneinfo.bed",
"QUALIMAP_INFO": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/qualimap_info.txt",
"KARYOBEDS": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/karyobeds/",
"KARYOPLOTER": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/karyoplot_gene_coordinates.txt",
"RSEMREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/rsemref/hg19_19",
"RRNALIST": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/hg19_19.rRNA_interval_list",
"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/GRCh37.p13.genome.d1.vd1.genome.fa",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/GRCh37.p13.genome.d1.vd1.genome.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/gencode.v19.annotation.gtf",
"GENOME_STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/STAR/2.7.6a/genome",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/annotate.genes.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/annotate.isoforms.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/refFlat.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/genes.ref.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/geneinfo.bed",
"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/qualimap_info.txt",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/karyobeds/",
"KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/karyoplot_gene_coordinates.txt",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/rsemref/hg19_19",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/hg19_19.rRNA_interval_list",
"ORGANISM": "hg19",
"TINREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg19/19/transcripts.protein_coding_only.bed12",
"TINREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_19/transcripts.protein_coding_only.bed12",
"FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_hg19_hs37d5_GRCh37_v2.0.0.tsv.gz",
"FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_hg19_hs37d5_GRCh37_v2.0.0.tsv",
"FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg19_hs37d5_GRCh37_v2.0.0.gff3"
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25 changes: 25 additions & 0 deletions config/genomes/biowulf/hg19_36.json
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@@ -0,0 +1,25 @@
{
"references": {
"rnaseq": {
"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/GRCh37.p13.genome.d1.vd1.genome.fa",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/GRCh37.p13.genome.d1.vd1.genome.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/gencode.v36lift37.annotation.gtf",
"GENOME_STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/STAR/2.7.6a/genome",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/annotate.genes.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/annotate.isoforms.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/refFlat.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/genes.ref.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/geneinfo.bed",
"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/qualimap_info.txt",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/karyobeds/",
"KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/karyoplot_gene_coordinates.txt",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/rsemref/hg19_36lift37",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/hg19_36lift37.rRNA_interval_list",
"ORGANISM": "hg19",
"TINREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg19_36lift37/transcripts.protein_coding_only.bed12",
"FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_hg19_hs37d5_GRCh37_v2.0.0.tsv.gz",
"FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_hg19_hs37d5_GRCh37_v2.0.0.tsv",
"FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg19_hs37d5_GRCh37_v2.0.0.gff3"
}
}
}
30 changes: 15 additions & 15 deletions config/genomes/biowulf/hg38_30.json
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@@ -1,22 +1,22 @@
{
"references": {
"rnaseq": {
"GENOMEFILE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/hg38.fa",
"GENOME": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/hg38.fa",
"GTFFILE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/30.gtf",
"GENOME_STARDIR": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/STAR/2.7.6a/genome",
"ANNOTATE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/annotate.genes.txt",
"ANNOTATEISOFORMS": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/annotate.isoforms.txt",
"REFFLAT": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/refFlat.txt",
"BEDREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/genes.ref.bed",
"GENEINFO": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/geneinfo.bed",
"QUALIMAP_INFO": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/qualimap_info.txt",
"KARYOBEDS": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/karyobeds/",
"KARYOPLOTER": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/karyoplot_gene_coordinates.txt",
"RSEMREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/rsemref/hg38_30",
"RRNALIST": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/hg38_30.rRNA_interval_list",
"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/GRCh38.d1.vd1.fa",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/GRCh38.d1.vd1.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/gencode.v30.primary_assembly.annotation.gtf",
"GENOME_STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/STAR/2.7.6a/genome",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/annotate.genes.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/annotate.isoforms.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/refFlat.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/genes.ref.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/geneinfo.bed",
"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/qualimap_info.txt",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/karyobeds/",
"KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/karyoplot_gene_coordinates.txt",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/rsemref/hg38_30",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/hg38_30.rRNA_interval_list",
"ORGANISM": "hg38",
"TINREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/30/transcripts.protein_coding_only.bed12",
"TINREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_30/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"
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30 changes: 15 additions & 15 deletions config/genomes/biowulf/hg38_34.json
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{
"references": {
"rnaseq": {
"GENOMEFILE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/hg38.fa",
"GENOME": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/hg38.fa",
"GTFFILE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/34.gtf",
"GENOME_STARDIR": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/STAR/2.7.6a/genome",
"ANNOTATE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/annotate.genes.txt",
"ANNOTATEISOFORMS": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/annotate.isoforms.txt",
"REFFLAT": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/refFlat.txt",
"BEDREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/genes.ref.bed",
"GENEINFO": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/geneinfo.bed",
"QUALIMAP_INFO": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/qualimap_info.txt",
"KARYOBEDS": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/karyobeds/",
"KARYOPLOTER": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/karyoplot_gene_coordinates.txt",
"RSEMREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/rsemref/hg38_34",
"RRNALIST": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/hg38_34.rRNA_interval_list",
"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/GRCh38.d1.vd1.fa",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/GRCh38.d1.vd1.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/gencode.v34.primary_assembly.annotation.gtf",
"GENOME_STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/STAR/2.7.6a/genome",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/annotate.genes.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/annotate.isoforms.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/refFlat.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/genes.ref.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/geneinfo.bed",
"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/qualimap_info.txt",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/karyobeds/",
"KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/karyoplot_gene_coordinates.txt",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/rsemref/hg38_34",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/hg38_34.rRNA_interval_list",
"ORGANISM": "hg38",
"TINREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/34/transcripts.protein_coding_only.bed12",
"TINREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_34/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"
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30 changes: 15 additions & 15 deletions config/genomes/biowulf/hg38_36.json
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{
"references": {
"rnaseq": {
"GENOMEFILE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/hg38.fa",
"GENOME": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/hg38.fa",
"GTFFILE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/36.gtf",
"GENOME_STARDIR": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/STAR/2.7.6a/genome",
"ANNOTATE": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/annotate.genes.txt",
"ANNOTATEISOFORMS": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/annotate.isoforms.txt",
"REFFLAT": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/refFlat.txt",
"BEDREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/genes.ref.bed",
"GENEINFO": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/geneinfo.bed",
"QUALIMAP_INFO": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/qualimap_info.txt",
"KARYOBEDS": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/karyobeds/",
"KARYOPLOTER": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/karyoplot_gene_coordinates.txt",
"RSEMREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/rsemref/hg38_36",
"RRNALIST": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/hg38_36.rRNA_interval_list",
"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/GRCh38.d1.vd1.fa",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/GRCh38.d1.vd1.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/gencode.v36.primary_assembly.annotation.gtf",
"GENOME_STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/STAR/2.7.6a/genome",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/annotate.genes.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/annotate.isoforms.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/refFlat.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/genes.ref.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/geneinfo.bed",
"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/qualimap_info.txt",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/karyobeds/",
"KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/karyoplot_gene_coordinates.txt",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/rsemref/hg38_36",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/hg38_36.rRNA_interval_list",
"ORGANISM": "hg38",
"TINREF": "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/RENEE/resources/hg38/36/transcripts.protein_coding_only.bed12",
"TINREF": "/data/CCBR_Pipeliner/db/PipeDB/GDC_refs/hg38_36/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"
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