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/*
vim: syntax=groovy
-*- mode: groovy;-*-
* -----------------------------------------------------
* Example Nextflow config file for using AWS-iGenomes
* -----------------------------------------------------
* Copy and paste the reference types that your pipeline needs.
* You can use the following code in your pipeline to get the paths:
*
* params.gtf = params.genome ? params.genomes[ params.genome ].gtf ?: false : false
* if (params.gtf) {
* Channel.fromPath(params.gtf)
* .ifEmpty { exit 1, "GTF annotation file not found: ${params.gtf}" }
* .into { my_gtf_channel }
* }
*
* The user can then specify --genome [key] or --gtf [path]
*
* If the references are synced to your local cluster, you can use a parallel config
* file for local files.
* For a working example of this, see https://github.com/SciLifeLab/NGI-RNAseq
*
* NB: Not all available references are listed here! eg. AbundantSequences,
* individual Chromosomes, SmallRNA, Variation and others.
*/
params {
// Command-line genome key
genome = false
// illumina iGenomes reference file paths on UPPMAX
genomes {
'GRCh37' {
bed12 = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/'
}
'GRCm38' {
bed12 = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/'
}
'TAIR10' {
bed12 = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/'
}
'EB2' {
bed12 = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/'
}
'UMD3.1' {
bed12 = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/'
}
'WBcel235' {
bed12 = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/'
}
'CanFam3.1' {
bed12 = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/'
}
'GRCz10' {
bed12 = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/'
}
'BDGP6' {
bed12 = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/'
}
'EquCab2' {
bed12 = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/'
}
'EB1' {
bed12 = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/'
}
'Galgal4' {
bed12 = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/'
}
'Gm01' {
bed12 = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/'
}
'Mmul_1' {
bed12 = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/'
}
'IRGSP-1.0' {
bed12 = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/'
}
'CHIMP2.1.4' {
bed12 = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/'
}
'Rnor_6.0' {
bed12 = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/'
}
'R64-1-1' {
bed12 = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/'
}
'EF2' {
bed12 = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/'
}
'Sbi1' {
bed12 = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/'
}
'Sscrofa10.2' {
bed12 = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/'
}
'AGPv3' {
bed12 = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed'
bismark = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex'
bowtie = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/BowtieIndex/genome'
bowtie2 = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/genome'
bwa = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa'
fasta = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta'
gtf = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf'
star = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/'
}
}
}