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Merged
rroutsong merged 4 commits into from
Mar 25, 2026
Merged

Bump release #128

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8a801b3
fix: bump VERSION
rroutsong Mar 25, 2026
f250d85
fix: move back to expected
rroutsong Mar 25, 2026
10b4c8d
fix: install toml snakevis without changing dir
rroutsong Mar 25, 2026
384b154
fix: update all configs with new artifacts
rroutsong Mar 25, 2026
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96 changes: 40 additions & 56 deletions .github/sv/configs/cfchip_norep_winput.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -92,107 +92,91 @@
"references": {
"hg19": {
"ALIAS": "hg19",
"SUPPORTED_PIPELINES": ["cfchip", "chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "/data/OpenOmics/references/chrom-seek/hg19_basic/indexes/hg19.blacklist.chrM",
"BWA": "/data/OpenOmics/references/chrom-seek/hg19_basic/indexes/hg19",
"EFFECTIVEGENOMESIZE": "2776919808",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/hg19/hg19_fantom.bed",
"FRAC": "0.8970265870106838",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/hg19_basic/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/hg19_basic/prot_gene_only.gtf",
"GENOME": "/data/OpenOmics/references/chrom-seek/hg19_basic/ref.fa",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/hg19_basic/genes.gtf",
"HOMER_REF": "/fdb/homer/genomes/hg19",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/hg19_basic/protein_coding_only.bed",
"REFLEN": "/data/OpenOmics/references/chrom-seek/hg19_basic/indexes/hg19.fa.sizes",
"FRAC": "0.8970265870106838",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "/fdb/meme/motif_databases/HUMAN/HOCOMOCOv11_full_HUMAN_mono_meme_format.meme",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/hg19_basic/indexes/hg19.fa.sizes",
"SUPPORTED_PIPELINES": [
"cfchip",
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/hg19/hg19_fantom.bed"
},
"hg38": {
"ALIAS": "hg38",
"SUPPORTED_PIPELINES": ["chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "/data/OpenOmics/references/chrom-seek/hg38_basic/indexes/hg38.blacklist.chrM",
"BWA": "/data/OpenOmics/references/chrom-seek/hg38_basic/indexes/hg38",
"EFFECTIVEGENOMESIZE": "2805636331",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/hg38_basic/enhancer/hg38_fantom.bed",
"FRAC": "0.9084767300375779",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/hg38_basic/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/hg38_basic/prot_gene_only.gtf",
"GENOME": "/data/OpenOmics/references/chrom-seek/hg38_basic/ref.fa",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/hg38_basic/genes.gtf",
"HOMER_REF": "/fdb/homer/genomes/hg38",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/hg38_basic/hg38.v48.cleaned.gtf",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/hg38_basic/protein_coding_only.bed",
"REFLEN": "/data/OpenOmics/references/chrom-seek/hg38_basic/indexes/hg38.fa.sizes",
"FRAC": "0.9084767300375779",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "/fdb/meme/motif_databases/HUMAN/HOCOMOCOv11_full_HUMAN_mono_meme_format.meme",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/hg38_basic/indexes/hg38.fa.sizes",
"SUPPORTED_PIPELINES": [
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/hg38_basic/enhancer/hg38_fantom.bed"
},
"mm10": {
"ALIAS": "mm10",
"SUPPORTED_PIPELINES": ["chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "/data/OpenOmics/references/chrom-seek/mm10_basic/indexes/mm10.blacklist.chrM.chr_rDNA",
"BWA": "/data/OpenOmics/references/chrom-seek/mm10_basic/indexes/mm10",
"EFFECTIVEGENOMESIZE": "2467481108",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/mm10_basic/enhancer/mm10_fantom.bed",
"FRAC": "0.9053190260640642",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/mm10_basic/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/mm10_basic/prot_gene_only.gtf",
"GENOME": "/data/OpenOmics/references/chrom-seek/mm10_basic/ref.fa",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/mm10_basic/genes.gtf",
"HOMER_REF": "/fdb/homer/genomes/mm10",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/mm10_basic/mm10.vM25.cleaned.gtf",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/mm10_basic/protein_coding_only.bed",
"REFLEN": "/data/OpenOmics/references/chrom-seek/mm10_basic/indexes/mm10.fa.sizes",
"FRAC": "0.9053190260640642",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "/fdb/meme/motif_databases/MOUSE/HOCOMOCOv11_full_MOUSE_mono_meme_format.meme",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/mm10_basic/indexes/mm10.fa.sizes",
"SUPPORTED_PIPELINES": [
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/mm10_basic/enhancer/mm10_fantom.bed"
},
"mm39": {
"ALIAS": "mm39",
"SUPPORTED_PIPELINES": ["chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "/data/OpenOmics/references/chrom-seek/mm39_basic/mm39.blacklist.chrM.fa",
"BWA": "/data/OpenOmics/references/chrom-seek/mm39_basic/GRCm39.primary_assembly.genome",
"EFFECTIVEGENOMESIZE": "2467473511",
"FRAC": "0.9375045835870026",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/mm39_basic/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/mm39_basic/prot_gene_only.gtf",
"GENOME": "/data/OpenOmics/references/chrom-seek/mm39_basic/GRCm39.primary_assembly.genome.fa.gz",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/mm39_basic/mm39.mM37.cleaned.gtf",
"HOMER_REF": "/fdb/homer/genomes/mm39",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/mm39_basic/protein_coding_only.bed",
"REFLEN": "/data/OpenOmics/references/chrom-seek/mm39_basic/GRCm39.primary_assembly.genome.sizes",
"FRAC": "0.9375045835870026",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "/fdb/meme/motif_databases/MOUSE/HOCOMOCOv11_full_MOUSE_mono_meme_format.meme",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/mm39_basic/GRCm39.primary_assembly.genome.sizes",
"SUPPORTED_PIPELINES": [
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer"
},
"rheMac10": {
"ALIAS": "rheMac10",
"SUPPORTED_PIPELINES": ["chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "",
"BWA": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr",
"EFFECTIVEGENOMESIZE": "2752365105",
"FRAC": "0.9643910116868353",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/rheMac10/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/rheMac10/prot_gene_only.gtf",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/rheMac10/protein_coding_only.bed",
"GENOME": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr.fa.gz",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.110.chr.genetype.gtf",
"HOMER_REF": "/fdb/homer/genomes/rheMac10",
"REFLEN": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr.sizes",
"FRAC": "0.9643910116868353",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr.sizes",
"SUPPORTED_PIPELINES": [
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer"
}
},
"samples": [
Expand Down
98 changes: 41 additions & 57 deletions .github/sv/configs/cfchip_wrep_winput.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -99,110 +99,94 @@
"version": "2.1.1",
"workpath": "/opt2/output"
},
"references": {
"references": {
"hg19": {
"ALIAS": "hg19",
"SUPPORTED_PIPELINES": ["cfchip", "chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "/data/OpenOmics/references/chrom-seek/hg19_basic/indexes/hg19.blacklist.chrM",
"BWA": "/data/OpenOmics/references/chrom-seek/hg19_basic/indexes/hg19",
"EFFECTIVEGENOMESIZE": "2776919808",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/hg19/hg19_fantom.bed",
"FRAC": "0.8970265870106838",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/hg19_basic/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/hg19_basic/prot_gene_only.gtf",
"GENOME": "/data/OpenOmics/references/chrom-seek/hg19_basic/ref.fa",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/hg19_basic/genes.gtf",
"HOMER_REF": "/fdb/homer/genomes/hg19",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/hg19_basic/protein_coding_only.bed",
"REFLEN": "/data/OpenOmics/references/chrom-seek/hg19_basic/indexes/hg19.fa.sizes",
"FRAC": "0.8970265870106838",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "/fdb/meme/motif_databases/HUMAN/HOCOMOCOv11_full_HUMAN_mono_meme_format.meme",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/hg19_basic/indexes/hg19.fa.sizes",
"SUPPORTED_PIPELINES": [
"cfchip",
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/hg19/hg19_fantom.bed"
},
"hg38": {
"ALIAS": "hg38",
"SUPPORTED_PIPELINES": ["chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "/data/OpenOmics/references/chrom-seek/hg38_basic/indexes/hg38.blacklist.chrM",
"BWA": "/data/OpenOmics/references/chrom-seek/hg38_basic/indexes/hg38",
"EFFECTIVEGENOMESIZE": "2805636331",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/hg38_basic/enhancer/hg38_fantom.bed",
"FRAC": "0.9084767300375779",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/hg38_basic/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/hg38_basic/prot_gene_only.gtf",
"GENOME": "/data/OpenOmics/references/chrom-seek/hg38_basic/ref.fa",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/hg38_basic/genes.gtf",
"HOMER_REF": "/fdb/homer/genomes/hg38",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/hg38_basic/hg38.v48.cleaned.gtf",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/hg38_basic/protein_coding_only.bed",
"REFLEN": "/data/OpenOmics/references/chrom-seek/hg38_basic/indexes/hg38.fa.sizes",
"FRAC": "0.9084767300375779",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "/fdb/meme/motif_databases/HUMAN/HOCOMOCOv11_full_HUMAN_mono_meme_format.meme",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/hg38_basic/indexes/hg38.fa.sizes",
"SUPPORTED_PIPELINES": [
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/hg38_basic/enhancer/hg38_fantom.bed"
},
"mm10": {
"ALIAS": "mm10",
"SUPPORTED_PIPELINES": ["chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "/data/OpenOmics/references/chrom-seek/mm10_basic/indexes/mm10.blacklist.chrM.chr_rDNA",
"BWA": "/data/OpenOmics/references/chrom-seek/mm10_basic/indexes/mm10",
"EFFECTIVEGENOMESIZE": "2467481108",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/mm10_basic/enhancer/mm10_fantom.bed",
"FRAC": "0.9053190260640642",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/mm10_basic/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/mm10_basic/prot_gene_only.gtf",
"GENOME": "/data/OpenOmics/references/chrom-seek/mm10_basic/ref.fa",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/mm10_basic/genes.gtf",
"HOMER_REF": "/fdb/homer/genomes/mm10",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/mm10_basic/mm10.vM25.cleaned.gtf",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/mm10_basic/protein_coding_only.bed",
"REFLEN": "/data/OpenOmics/references/chrom-seek/mm10_basic/indexes/mm10.fa.sizes",
"FRAC": "0.9053190260640642",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "/fdb/meme/motif_databases/MOUSE/HOCOMOCOv11_full_MOUSE_mono_meme_format.meme",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/mm10_basic/indexes/mm10.fa.sizes",
"SUPPORTED_PIPELINES": [
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer",
"ENHANCER": "/data/OpenOmics/references/chrom-seek/mm10_basic/enhancer/mm10_fantom.bed"
},
"mm39": {
"ALIAS": "mm39",
"SUPPORTED_PIPELINES": ["chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "/data/OpenOmics/references/chrom-seek/mm39_basic/mm39.blacklist.chrM.fa",
"BWA": "/data/OpenOmics/references/chrom-seek/mm39_basic/GRCm39.primary_assembly.genome",
"EFFECTIVEGENOMESIZE": "2467473511",
"FRAC": "0.9375045835870026",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/mm39_basic/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/mm39_basic/prot_gene_only.gtf",
"GENOME": "/data/OpenOmics/references/chrom-seek/mm39_basic/GRCm39.primary_assembly.genome.fa.gz",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/mm39_basic/mm39.mM37.cleaned.gtf",
"HOMER_REF": "/fdb/homer/genomes/mm39",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/mm39_basic/protein_coding_only.bed",
"REFLEN": "/data/OpenOmics/references/chrom-seek/mm39_basic/GRCm39.primary_assembly.genome.sizes",
"FRAC": "0.9375045835870026",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "/fdb/meme/motif_databases/MOUSE/HOCOMOCOv11_full_MOUSE_mono_meme_format.meme",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/mm39_basic/GRCm39.primary_assembly.genome.sizes",
"SUPPORTED_PIPELINES": [
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer"
},
"rheMac10": {
"ALIAS": "rheMac10",
"SUPPORTED_PIPELINES": ["chip", "atac", "cutnrun"],
"BLACKLISTBWAINDEX": "",
"BWA": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr",
"EFFECTIVEGENOMESIZE": "2752365105",
"FRAC": "0.9643910116868353",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/rheMac10/geneinfo.bed",
"GENEINFO": "/data/OpenOmics/references/chrom-seek/rheMac10/prot_gene_only.gtf",
"PROTEIN_CODING_BED": "/data/OpenOmics/references/chrom-seek/rheMac10/protein_coding_only.bed",
"GENOME": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr.fa.gz",
"GTFFILE": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.110.chr.genetype.gtf",
"HOMER_REF": "/fdb/homer/genomes/rheMac10",
"REFLEN": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr.sizes",
"FRAC": "0.9643910116868353",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"MEME_EUKARYOTE_DB": "/fdb/meme/motif_databases/EUKARYOTE/jolma2013.meme",
"MEME_GENOME_DB": "",
"MEME_VERTEBRATES_DB": "/fdb/meme/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme",
"REFLEN": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr.sizes",
"SUPPORTED_PIPELINES": [
"chip",
"atac",
"cutnrun"
]
"HOMER_REF": "/fdb/homer"
}
},
"samples": [
Expand Down
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