diff --git a/.github/sv/configs/cfchip_norep_winput.json b/.github/sv/configs/cfchip_norep_winput.json index c447f46..795b817 100644 --- a/.github/sv/configs/cfchip_norep_winput.json +++ b/.github/sv/configs/cfchip_norep_winput.json @@ -13,11 +13,12 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3", + "preseq": "docker://rroutsong/preseq:0.0.1", "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { @@ -92,107 +93,91 @@ "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": [ diff --git a/.github/sv/configs/cfchip_wrep_winput.json b/.github/sv/configs/cfchip_wrep_winput.json index 9e5fc12..047ef4c 100644 --- a/.github/sv/configs/cfchip_wrep_winput.json +++ b/.github/sv/configs/cfchip_wrep_winput.json @@ -7,11 +7,12 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3", + "preseq": "docker://rroutsong/preseq:0.0.1", "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { @@ -99,110 +100,94 @@ "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": [ diff --git a/.github/sv/configs/chip_paired_norep_noinput.json b/.github/sv/configs/chip_paired_norep_noinput.json index e1c6592..7698d58 100644 --- a/.github/sv/configs/chip_paired_norep_noinput.json +++ b/.github/sv/configs/chip_paired_norep_noinput.json @@ -13,11 +13,12 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3", + "preseq": "docker://rroutsong/preseq:0.0.1", "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { @@ -88,107 +89,91 @@ "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": [ diff --git a/.github/sv/configs/chip_paired_norep_winput.json b/.github/sv/configs/chip_paired_norep_winput.json index 76bfc4e..a3f3c12 100644 --- a/.github/sv/configs/chip_paired_norep_winput.json +++ b/.github/sv/configs/chip_paired_norep_winput.json @@ -13,12 +13,13 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "multiqc": "docker://multiqc/multiqc:v1.32", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3" + "preseq": "docker://rroutsong/preseq:0.0.1", + "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { "assay": "chip", @@ -92,107 +93,91 @@ "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": [ diff --git a/.github/sv/configs/chip_paired_wrep_noinput.json b/.github/sv/configs/chip_paired_wrep_noinput.json index 6b8542e..76806b3 100644 --- a/.github/sv/configs/chip_paired_wrep_noinput.json +++ b/.github/sv/configs/chip_paired_wrep_noinput.json @@ -13,11 +13,12 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3", + "preseq": "docker://rroutsong/preseq:0.0.1", "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { @@ -100,107 +101,91 @@ "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": [ diff --git a/.github/sv/configs/chip_paired_wrep_winput.json b/.github/sv/configs/chip_paired_wrep_winput.json index 6b8542e..76806b3 100644 --- a/.github/sv/configs/chip_paired_wrep_winput.json +++ b/.github/sv/configs/chip_paired_wrep_winput.json @@ -13,11 +13,12 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3", + "preseq": "docker://rroutsong/preseq:0.0.1", "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { @@ -100,107 +101,91 @@ "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": [ diff --git a/.github/sv/configs/chip_single_norep_noinput.json b/.github/sv/configs/chip_single_norep_noinput.json index 3030dab..a276f58 100644 --- a/.github/sv/configs/chip_single_norep_noinput.json +++ b/.github/sv/configs/chip_single_norep_noinput.json @@ -13,11 +13,12 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3", + "preseq": "docker://rroutsong/preseq:0.0.1", "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { @@ -88,107 +89,91 @@ "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": [ diff --git a/.github/sv/configs/chip_single_norep_winput.json b/.github/sv/configs/chip_single_norep_winput.json index 9fabdb2..a276f58 100644 --- a/.github/sv/configs/chip_single_norep_winput.json +++ b/.github/sv/configs/chip_single_norep_winput.json @@ -13,12 +13,13 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "multiqc": "docker://multiqc/multiqc:v1.32", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3" + "preseq": "docker://rroutsong/preseq:0.0.1", + "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { "assay": "chip", @@ -88,107 +89,91 @@ "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": [ diff --git a/.github/sv/configs/chip_single_wrep_noinput.json b/.github/sv/configs/chip_single_wrep_noinput.json index ae8b449..e75d857 100644 --- a/.github/sv/configs/chip_single_wrep_noinput.json +++ b/.github/sv/configs/chip_single_wrep_noinput.json @@ -13,12 +13,13 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "multiqc": "docker://multiqc/multiqc:v1.32", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3" + "preseq": "docker://rroutsong/preseq:0.0.1", + "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { "assay": "chip", @@ -96,107 +97,91 @@ "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": [ diff --git a/.github/sv/configs/chip_single_wrep_winput.json b/.github/sv/configs/chip_single_wrep_winput.json index db2b773..878c647 100644 --- a/.github/sv/configs/chip_single_wrep_winput.json +++ b/.github/sv/configs/chip_single_wrep_winput.json @@ -13,12 +13,13 @@ "images": { "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0", "diffbind": "docker://skchronicles/cfchip_toolkit:v0.5.0", - "multiqc": "docker://multiqc/multiqc:v1.32", - "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", - "preseq": "docker://rroutsong/preseq:0.0.1", + "uropa": "docker://rroutsong/uropa:4.0.3", "python": "docker://rroutsong/chrom_seek_python:0.1.3", + "homer-4": "docker://rroutsong/homer-motif:0.0.1", + "ppqt": "docker://seqeralabs/phantompeakqualtools:latest", "seacr": "docker://rroutsong/seacr:0.0.1", - "uropa": "docker://rroutsong/uropa:4.0.3" + "preseq": "docker://rroutsong/preseq:0.0.1", + "multiqc": "docker://multiqc/multiqc:v1.32" }, "options": { "assay": "chip", @@ -100,107 +101,91 @@ "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": [ diff --git a/.github/workflows/auto-release.yml b/.github/workflows/auto-release.yml index 2ec4c2f..dc14fcc 100644 --- a/.github/workflows/auto-release.yml +++ b/.github/workflows/auto-release.yml @@ -24,7 +24,7 @@ jobs: run: | python -m pip install --upgrade pip git clone https://github.com/OpenOmics/snakevision.git $GITHUB_WORKSPACE/vis - cd $GITHUB_WORKSPACE/vis; pip install . + pip install $GITHUB_WORKSPACE/vis pip install -r .github/release_reqs.txt echo "$GITHUB_WORKSPACE/vis/bin" >> $GITHUB_PATH diff --git a/config/genome.json b/config/genome.json index f8944a3..16b7535 100644 --- a/config/genome.json +++ b/config/genome.json @@ -78,6 +78,7 @@ "BWA": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr", "EFFECTIVEGENOMESIZE": "2752365105", "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", "REFLEN": "/data/OpenOmics/references/chrom-seek/rheMac10/Macaca_mulatta.Mmul_10.dna.chr.sizes",