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Merge pull request #675 from maxplanck-ie/dev_ksikora2
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updated organims yamls with correct STAR index versions
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@katsikora
katsikora committed Aug 24, 2020
2 parents 2af919d + c633339 commit 8d00da0
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Showing 8 changed files with 8 additions and 8 deletions.
2 changes: 1 addition & 1 deletion snakePipes/shared/organisms/GRCz10.yaml
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Expand Up @@ -7,7 +7,7 @@ hisat2_index: "/data/repository/organisms/GRCz10_ensembl/HISAT2Index/genome"
bwa_index: "/data/repository/organisms/GRCz10_ensembl/BWAindex/genome.fa"
bwameth_index: "/data/repository/organisms/GRCz10_ensembl/BWAmethIndex/genome.fa"
known_splicesites: "/data/repository/organisms/GRCz10_ensembl/ensembl/release-88/HISAT2/splice_sites.txt"
star_index: "/data/repository/organisms/GRCz10_ensembl/STARIndex/2.7.1a/"
star_index: "/data/repository/organisms/GRCz10_ensembl/STARIndex/2.7.4a/"
genes_bed: "/data/repository/organisms/GRCz10_ensembl/ensembl/release-88/genes.bed"
genes_gtf: "/data/repository/organisms/GRCz10_ensembl/ensembl/release-88/genes.gtf"
extended_coding_regions_gtf: "/data/repository/organisms/GRCz10_ensembl/ensembl/release-88/genes.slop.gtf"
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2 changes: 1 addition & 1 deletion snakePipes/shared/organisms/SchizoSPombe_ASM294v2.yaml
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Expand Up @@ -6,7 +6,7 @@ bowtie2_index: "/data/repository/organisms/SchizoSPombe_ASM294v2_ensembl/BowtieI
hisat2_index: "/data/repository/organisms/SchizoSPombe_ASM294v2_ensembl/HISAT2Index/genome"
bwa_index: "/data/repository/organisms/SchizoSPombe_ASM294v2_ensembl/BWAindex/genome.fa"
known_splicesites: "/data/repository/organisms/SchizoSPombe_ASM294v2_ensembl/ensembl/release-35/HISAT2/splice_sites.txt"
star_index: "/data/repository/organisms/SchizoSPombe_ASM294v2_ensembl/STARIndex/2.7.1a/"
star_index: "/data/repository/organisms/SchizoSPombe_ASM294v2_ensembl/STARIndex/2.7.4a/"
genes_bed: "/data/repository/organisms/SchizoSPombe_ASM294v2_ensembl/Ensembl/release-35/genes.bed"
genes_gtf: "/data/repository/organisms/SchizoSPombe_ASM294v2_ensembl/Ensembl/release-35/genes.gtf"
extended_coding_regions_gtf: "/data/repository/organisms/SchizoSPombe_ASM294v2_ensembl/Ensembl/release-35/genes.slop.gtf"
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2 changes: 1 addition & 1 deletion snakePipes/shared/organisms/dm3.yaml
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Expand Up @@ -6,7 +6,7 @@ bowtie2_index: "/data/repository/organisms/dm3_ensembl/BowtieIndex/genome"
hisat2_index: "/data/repository/organisms/dm3_ensembl/HISAT2Index/genome"
bwa_index: "/data/repository/organisms/dm3_ensembl/BWAindex/genome.fa"
known_splicesites: "/data/repository/organisms/dm3_ensembl/ensembl/release-78/HISAT2/splice_sites.txt"
star_index: "/data/repository/organisms/dm3_ensembl/STARIndex/2.7.1a/"
star_index: "/data/repository/organisms/dm3_ensembl/STARIndex/2.7.4a/"
genes_bed: "/data/repository/organisms/dm3_ensembl/Ensembl/release-78/genes.bed"
genes_gtf: "/data/repository/organisms/dm3_ensembl/Ensembl/release-78/genes.gtf"
extended_coding_regions_gtf: "/data/repository/organisms/dm3_ensembl/Ensembl/release-78/genes.slop.gtf"
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2 changes: 1 addition & 1 deletion snakePipes/shared/organisms/dm6.yaml
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Expand Up @@ -6,7 +6,7 @@ bowtie2_index: "/data/repository/organisms/dm6_ensembl/BowtieIndex/genome"
hisat2_index: "/data/repository/organisms/dm6_ensembl/HISAT2Index/genome"
bwa_index: "/data/repository/organisms/dm6_ensembl/BWAindex/genome.fa"
known_splicesites: "/data/repository/organisms/dm6_ensembl/ensembl/release-79/HISAT2/splice_sites.txt"
star_index: "/data/repository/organisms/dm6_ensembl/STARIndex/2.7.1a/"
star_index: "/data/repository/organisms/dm6_ensembl/STARIndex/2.7.4a/"
genes_bed: "/data/repository/organisms/dm6_ensembl/Ensembl/release-79/genes.bed"
genes_gtf: "/data/repository/organisms/dm6_ensembl/Ensembl/release-79/genes.gtf"
extended_coding_regions_gtf: "/data/repository/organisms/dm6_ensembl/Ensembl/release-79/genes.slop.gtf"
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2 changes: 1 addition & 1 deletion snakePipes/shared/organisms/hg38.yaml
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Expand Up @@ -6,7 +6,7 @@ bowtie2_index: "/data/repository/organisms/GRCh38_ensembl/BowtieIndex/genome"
hisat2_index: "/data/repository/organisms/GRCh38_ensembl/HISAT2Index/genome"
bwa_index: "/data/repository/organisms/GRCh38_ensembl/BWAindex/genome.fa"
known_splicesites: "/data/repository/organisms/GRCh38_ensembl/gencode/release_27/HISAT2/splice_sites.txt"
star_index: "/data/repository/organisms/GRCh38_ensembl/STARIndex/2.7.1a/"
star_index: "/data/repository/organisms/GRCh38_ensembl/STARIndex/2.7.4a/"
genes_bed: "/data/repository/organisms/GRCh38_ensembl/gencode/release_27/genes.bed"
genes_gtf: "/data/repository/organisms/GRCh38_ensembl/gencode/release_27/genes.gtf"
extended_coding_regions_gtf: "/data/repository/organisms/GRCh38_ensembl/gencode/release_27/genes.slop.gtf"
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2 changes: 1 addition & 1 deletion snakePipes/shared/organisms/hs37d5.yaml
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Expand Up @@ -6,7 +6,7 @@ bowtie2_index: "/data/repository/organisms/hs37d5_ensembl/BowtieIndex/genome"
hisat2_index: "/data/repository/organisms/hs37d5_ensembl/HISAT2Index/genome"
bwa_index: "/data/repository/organisms/hs37d5_ensembl/BWAindex/genome.fa"
known_splicesites: "/data/repository/organisms/hs37d5_ensembl/gencode/release_19/HISAT2/splice_sites.txt"
star_index: "/data/repository/organisms/hs37d5_ensembl/STARIndex/2.7.1a/"
star_index: "/data/repository/organisms/hs37d5_ensembl/STARIndex/2.7.4a/"
genes_bed: "/data/repository/organisms/hs37d5_ensembl/gencode/release_19/genes.bed"
genes_gtf: "/data/repository/organisms/hs37d5_ensembl/gencode/release_19/genes.gtf"
extended_coding_regions_gtf: "/data/repository/organisms/hs37d5_ensembl/gencode/release_19/genes.slop.gtf"
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2 changes: 1 addition & 1 deletion snakePipes/shared/organisms/mm10_gencodeM13.yaml
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Expand Up @@ -6,7 +6,7 @@ bowtie2_index: "/data/repository/organisms/GRCm38_ensembl/BowtieIndex/genome"
hisat2_index: "/data/repository/organisms/GRCm38_ensembl/HISAT2Index/genome"
bwa_index: "/data/repository/organisms/GRCm38_ensembl/BWAindex/genome.fa"
known_splicesites: "/data/repository/organisms/GRCm38_ensembl/gencode/m13/HISAT2/splice_sites.txt"
star_index: "/data/repository/organisms/GRCm38_ensembl/STARIndex/2.7.1a/"
star_index: "/data/repository/organisms/GRCm38_ensembl/STARIndex/2.7.4a/"
genes_bed: "/data/repository/organisms/GRCm38_ensembl/gencode/m13/genes.bed"
genes_gtf: "/data/repository/organisms/GRCm38_ensembl/gencode/m13/genes.gtf"
extended_coding_regions_gtf: "/data/repository/organisms/GRCm38_ensembl/gencode/m13/genes.slop.gtf"
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2 changes: 1 addition & 1 deletion snakePipes/shared/organisms/mm9.yaml
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Expand Up @@ -6,7 +6,7 @@ bowtie2_index: "/data/repository/organisms/GRCm37_ensembl/BowtieIndex/genome"
hisat2_index: "/data/repository/organisms/GRCm37_ensembl/HISAT2Index/genome"
bwa_index: "/data/repository/organisms/GRCm37_ensembl/BWAindex/genome.fa"
known_splicesites: "/data/repository/organisms/GRCm37_ensembl/gencode/m1/HISAT2/splice_sites.txt"
star_index: "/data/repository/organisms/GRCm37_ensembl/STARIndex/2.7.1a/"
star_index: "/data/repository/organisms/GRCm37_ensembl/STARIndex/2.7.4a/"
genes_bed: "/data/repository/organisms/GRCm37_ensembl/gencode/m1/genes.bed"
genes_gtf: "/data/repository/organisms/GRCm37_ensembl/gencode/m1/genes.gtf"
extended_coding_regions_gtf: "/data/repository/organisms/GRCm37_ensembl/gencode/m1/genes.slop.gtf"
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