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| a | b/conf/igenomes.config | ||
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| 1 | /* |
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| 2 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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| 3 | Nextflow config file for iGenomes paths |
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| 4 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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| 5 | Defines reference genomes using iGenome paths. |
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| 6 | Can be used by any config that customises the base path using: |
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| 7 | $params.igenomes_base / --igenomes_base |
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| 8 | ---------------------------------------------------------------------------------------- |
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| 9 | */ |
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| 10 | |||
| 11 | params { |
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| 12 | // illumina iGenomes reference file paths |
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| 13 | genomes { |
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| 14 | 'GRCh37' { |
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| 15 | fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" |
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| 16 | bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" |
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| 17 | bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" |
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| 18 | star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" |
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| 19 | bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" |
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| 20 | gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" |
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| 21 | bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" |
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| 22 | readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" |
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| 23 | mito_name = "MT" |
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| 24 | blacklist = "${projectDir}/assets/blacklists/v1.0/GRCh37-blacklist.v1.bed" |
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| 25 | macs_gsize = [ |
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| 26 | "50" : 2684219875, |
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| 27 | "75" : 2733035409, |
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| 28 | "100" : 2774803719, |
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| 29 | "150" : 2824648687, |
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| 30 | "200" : 2848794782 |
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| 31 | ] |
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| 32 | } |
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| 33 | 'GRCh38' { |
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| 34 | fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" |
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| 35 | bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" |
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| 36 | bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" |
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| 37 | star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" |
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| 38 | bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" |
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| 39 | gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" |
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| 40 | bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" |
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| 41 | mito_name = "chrM" |
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| 42 | blacklist = "${projectDir}/assets/blacklists/v3.0/hg38-blacklist.v3.bed" |
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| 43 | macs_gsize = [ |
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| 44 | "50" : 2701262066, |
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| 45 | "75" : 2749859687, |
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| 46 | "100" : 2805665311, |
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| 47 | "150" : 2862089864, |
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| 48 | "200" : 2892537351 |
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| 49 | ] |
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| 50 | } |
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| 51 | 'CHM13' { |
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| 52 | fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" |
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| 53 | bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" |
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| 54 | bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" |
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| 55 | gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" |
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| 56 | gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" |
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| 57 | mito_name = "chrM" |
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| 58 | } |
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| 59 | 'GRCm38' { |
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| 60 | fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" |
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| 61 | bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" |
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| 62 | bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" |
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| 63 | star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" |
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| 64 | bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" |
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| 65 | gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" |
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| 66 | bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" |
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| 67 | readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" |
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| 68 | mito_name = "MT" |
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| 69 | blacklist = "${projectDir}/assets/blacklists/v2.0/GRCm38-blacklist.v2.bed" |
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| 70 | macs_gsize = [ |
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| 71 | "50" : 2307679482, |
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| 72 | "75" : 2406655830, |
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| 73 | "100" : 2466184610, |
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| 74 | "150" : 2492306232, |
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| 75 | "200" : 2519386924 |
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| 76 | ] |
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| 77 | } |
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| 78 | 'TAIR10' { |
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| 79 | fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" |
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| 80 | bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" |
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| 81 | bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" |
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| 82 | star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" |
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| 83 | bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" |
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| 84 | gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" |
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| 85 | bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" |
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| 86 | readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" |
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| 87 | mito_name = "Mt" |
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| 88 | macs_gsize = [ |
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| 89 | "50" : 114339094, |
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| 90 | "75" : 115317469, |
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| 91 | "100" : 118459858, |
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| 92 | "150" : 118504138, |
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| 93 | "200" : 117723393 |
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| 94 | ] |
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| 95 | } |
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| 96 | 'EB2' { |
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| 97 | fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" |
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| 98 | bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" |
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| 99 | bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" |
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| 100 | star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" |
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| 101 | bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" |
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| 102 | gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" |
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| 103 | bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" |
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| 104 | readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" |
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| 105 | macs_gsize = [ |
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| 106 | "50" : 4150072, |
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| 107 | "75" : 4191132, |
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| 108 | "100" : 4198752, |
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| 109 | "150" : 4176800, |
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| 110 | "200" : 4197072 |
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| 111 | ] |
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| 112 | } |
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| 113 | 'UMD3.1' { |
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| 114 | fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" |
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| 115 | bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" |
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| 116 | bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" |
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| 117 | star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" |
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| 118 | bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" |
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| 119 | gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" |
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| 120 | bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" |
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| 121 | readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" |
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| 122 | mito_name = "MT" |
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| 123 | macs_gsize = [ |
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| 124 | "50" : 2370644326, |
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| 125 | "75" : 2480511357, |
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| 126 | "100" : 2567220492, |
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| 127 | "150" : 2594494201, |
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| 128 | "200" : 2648740387 |
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| 129 | ] |
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| 130 | } |
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| 131 | 'WBcel235' { |
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| 132 | fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" |
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| 133 | bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" |
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| 134 | bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" |
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| 135 | star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" |
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| 136 | bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" |
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| 137 | gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" |
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| 138 | bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" |
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| 139 | mito_name = "MtDNA" |
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| 140 | macs_gsize = [ |
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| 141 | "50" : 95159402, |
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| 142 | "75" : 96945370, |
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| 143 | "100" : 98259898, |
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| 144 | "150" : 98721103, |
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| 145 | "200" : 98672558 |
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| 146 | ] |
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| 147 | } |
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| 148 | 'CanFam3.1' { |
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| 149 | fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" |
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| 150 | bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" |
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| 151 | bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" |
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| 152 | star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" |
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| 153 | bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" |
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| 154 | gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" |
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| 155 | bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" |
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| 156 | readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" |
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| 157 | mito_name = "MT" |
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| 158 | macs_gsize = [ |
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| 159 | "50" : 2237684358, |
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| 160 | "75" : 2279860111, |
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| 161 | "100" : 2293979635, |
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| 162 | "150" : 2300527794, |
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| 163 | "200" : 2313332891 |
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| 164 | ] |
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| 165 | } |
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| 166 | 'GRCz10' { |
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| 167 | fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" |
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| 168 | bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" |
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| 169 | bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" |
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| 170 | star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" |
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| 171 | bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" |
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| 172 | gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" |
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| 173 | bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" |
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| 174 | mito_name = "MT" |
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| 175 | macs_gsize = [ |
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| 176 | "50" : 1172895610, |
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| 177 | "75" : 1229400206, |
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| 178 | "100" : 1253908756, |
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| 179 | "150" : 1285330773, |
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| 180 | "200" : 1292538906 |
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| 181 | ] |
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| 182 | } |
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| 183 | 'BDGP6' { |
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| 184 | fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" |
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| 185 | bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" |
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| 186 | bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" |
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| 187 | star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" |
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| 188 | bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" |
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| 189 | gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" |
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| 190 | bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" |
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| 191 | mito_name = "M" |
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| 192 | macs_gsize = [ |
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| 193 | "50" : 123519388, |
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| 194 | "75" : 124886264, |
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| 195 | "100" : 126807034, |
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| 196 | "150" : 126903604, |
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| 197 | "200" : 128575605 |
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| 198 | ] |
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| 199 | } |
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| 200 | 'EquCab2' { |
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| 201 | fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" |
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| 202 | bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" |
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| 203 | bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" |
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| 204 | star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" |
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| 205 | bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" |
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| 206 | gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" |
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| 207 | bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" |
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| 208 | readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" |
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| 209 | mito_name = "MT" |
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| 210 | macs_gsize = [ |
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| 211 | "50" : 2294980416, |
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| 212 | "75" : 2289244826, |
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| 213 | "100" : 2334155865, |
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| 214 | "150" : 2343297042, |
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| 215 | "200" : 2350515523 |
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| 216 | ] |
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| 217 | } |
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| 218 | 'EB1' { |
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| 219 | fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" |
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| 220 | bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" |
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| 221 | bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" |
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| 222 | star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" |
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| 223 | bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" |
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| 224 | gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" |
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| 225 | bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" |
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| 226 | readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" |
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| 227 | macs_gsize = [ |
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| 228 | "50" : 4481912, |
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| 229 | "75" : 4485018, |
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| 230 | "100" : 4468952, |
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| 231 | "150" : 4489684, |
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| 232 | "200" : 4527891 |
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| 233 | ] |
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| 234 | } |
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| 235 | 'Galgal4' { |
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| 236 | fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" |
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| 237 | bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" |
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| 238 | bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" |
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| 239 | star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" |
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| 240 | bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" |
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| 241 | gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" |
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| 242 | bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" |
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| 243 | mito_name = "MT" |
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| 244 | macs_gsize = [ |
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| 245 | "50" : 974987959, |
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| 246 | "75" : 978772437, |
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| 247 | "100" : 984935167, |
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| 248 | "150" : 979442039, |
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| 249 | "200" : 991678648 |
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| 250 | ] |
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| 251 | } |
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| 252 | 'Gm01' { |
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| 253 | fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" |
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| 254 | bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" |
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| 255 | bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" |
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| 256 | star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" |
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| 257 | bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" |
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| 258 | gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" |
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| 259 | bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" |
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| 260 | readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" |
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| 261 | macs_gsize = [ |
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| 262 | "50" : 748112428, |
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| 263 | "75" : 826455017, |
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| 264 | "100" : 857283568, |
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| 265 | "150" : 895077451, |
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| 266 | "200" : 911783687 |
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| 267 | ] |
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| 268 | } |
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| 269 | 'Mmul_1' { |
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| 270 | fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" |
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| 271 | bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" |
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| 272 | bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" |
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| 273 | star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" |
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| 274 | bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" |
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| 275 | gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" |
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| 276 | bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" |
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| 277 | readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" |
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| 278 | mito_name = "MT" |
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| 279 | macs_gsize = [ |
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| 280 | "50" : 2498932238, |
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| 281 | "75" : 2598624693, |
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| 282 | "100" : 2642166663, |
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| 283 | "150" : 2661433343, |
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| 284 | "200" : 2674888870 |
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| 285 | ] |
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| 286 | } |
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| 287 | 'IRGSP-1.0' { |
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| 288 | fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" |
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| 289 | bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" |
||
| 290 | bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" |
||
| 291 | star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" |
||
| 292 | bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" |
||
| 293 | gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" |
||
| 294 | bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" |
||
| 295 | mito_name = "Mt" |
||
| 296 | macs_gsize = [ |
||
| 297 | "50" : 322594956, |
||
| 298 | "75" : 337043804, |
||
| 299 | "100" : 345775274, |
||
| 300 | "150" : 355020671, |
||
| 301 | "200" : 363478234 |
||
| 302 | ] |
||
| 303 | } |
||
| 304 | 'CHIMP2.1.4' { |
||
| 305 | fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" |
||
| 306 | bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" |
||
| 307 | bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" |
||
| 308 | star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" |
||
| 309 | bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" |
||
| 310 | gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" |
||
| 311 | bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" |
||
| 312 | readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" |
||
| 313 | mito_name = "MT" |
||
| 314 | macs_gsize = [ |
||
| 315 | "50" : 2576111695, |
||
| 316 | "75" : 2702821987, |
||
| 317 | "100" : 2733435831, |
||
| 318 | "150" : 2735167196, |
||
| 319 | "200" : 2738912507 |
||
| 320 | ] |
||
| 321 | } |
||
| 322 | 'Rnor_5.0' { |
||
| 323 | fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" |
||
| 324 | bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" |
||
| 325 | bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" |
||
| 326 | star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" |
||
| 327 | bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" |
||
| 328 | gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" |
||
| 329 | bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" |
||
| 330 | mito_name = "MT" |
||
| 331 | macs_gsize = [ |
||
| 332 | "50" : 2303951475, |
||
| 333 | "75" : 2367071843, |
||
| 334 | "100" : 2402745922, |
||
| 335 | "150" : 2405692811, |
||
| 336 | "200" : 2407324495 |
||
| 337 | ] |
||
| 338 | } |
||
| 339 | 'Rnor_6.0' { |
||
| 340 | fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" |
||
| 341 | bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" |
||
| 342 | bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" |
||
| 343 | star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" |
||
| 344 | bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" |
||
| 345 | gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" |
||
| 346 | bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" |
||
| 347 | mito_name = "MT" |
||
| 348 | macs_gsize = [ |
||
| 349 | "50" : 2375372135, |
||
| 350 | "75" : 2440746491, |
||
| 351 | "100" : 2480029900, |
||
| 352 | "150" : 2477334634, |
||
| 353 | "200" : 2478552171 |
||
| 354 | ] |
||
| 355 | } |
||
| 356 | 'R64-1-1' { |
||
| 357 | fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" |
||
| 358 | bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" |
||
| 359 | bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" |
||
| 360 | star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" |
||
| 361 | bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" |
||
| 362 | gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" |
||
| 363 | bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" |
||
| 364 | mito_name = "MT" |
||
| 365 | macs_gsize = [ |
||
| 366 | "50" : 11624332, |
||
| 367 | "75" : 11693438, |
||
| 368 | "100" : 11777680, |
||
| 369 | "150" : 11783749, |
||
| 370 | "200" : 11825681 |
||
| 371 | ] |
||
| 372 | } |
||
| 373 | 'EF2' { |
||
| 374 | fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" |
||
| 375 | bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" |
||
| 376 | bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" |
||
| 377 | star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" |
||
| 378 | bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" |
||
| 379 | gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" |
||
| 380 | bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" |
||
| 381 | readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" |
||
| 382 | mito_name = "MT" |
||
| 383 | macs_gsize = [ |
||
| 384 | "50" : 12190646, |
||
| 385 | "75" : 12291456, |
||
| 386 | "100" : 12346649, |
||
| 387 | "150" : 12403911, |
||
| 388 | "200" : 12442064 |
||
| 389 | ] |
||
| 390 | } |
||
| 391 | 'Sbi1' { |
||
| 392 | fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" |
||
| 393 | bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" |
||
| 394 | bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" |
||
| 395 | star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" |
||
| 396 | bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" |
||
| 397 | gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" |
||
| 398 | bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" |
||
| 399 | readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" |
||
| 400 | macs_gsize = [ |
||
| 401 | "50" : 444102512, |
||
| 402 | "75" : 506986021, |
||
| 403 | "100" : 540037446, |
||
| 404 | "150" : 575130820, |
||
| 405 | "200" : 595857042 |
||
| 406 | ] |
||
| 407 | } |
||
| 408 | 'Sscrofa10.2' { |
||
| 409 | fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" |
||
| 410 | bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" |
||
| 411 | bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" |
||
| 412 | star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" |
||
| 413 | bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" |
||
| 414 | gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" |
||
| 415 | bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" |
||
| 416 | readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" |
||
| 417 | mito_name = "MT" |
||
| 418 | macs_gsize = [ |
||
| 419 | "50" : 2105185708, |
||
| 420 | "75" : 2131615607, |
||
| 421 | "100" : 2149244400, |
||
| 422 | "150" : 2189757848, |
||
| 423 | "200" : 2203893315 |
||
| 424 | ] |
||
| 425 | } |
||
| 426 | 'AGPv3' { |
||
| 427 | fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" |
||
| 428 | bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" |
||
| 429 | bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" |
||
| 430 | star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" |
||
| 431 | bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" |
||
| 432 | gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" |
||
| 433 | bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" |
||
| 434 | mito_name = "Mt" |
||
| 435 | macs_gsize = [ |
||
| 436 | "50" : 1113453752, |
||
| 437 | "75" : 1392458449, |
||
| 438 | "100" : 1579923466, |
||
| 439 | "150" : 1729475311, |
||
| 440 | "200" : 1841419596 |
||
| 441 | ] |
||
| 442 | } |
||
| 443 | 'hg38' { |
||
| 444 | fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" |
||
| 445 | bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" |
||
| 446 | bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" |
||
| 447 | star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" |
||
| 448 | bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" |
||
| 449 | gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" |
||
| 450 | bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" |
||
| 451 | mito_name = "chrM" |
||
| 452 | blacklist = "${projectDir}/assets/blacklists/v3.0/hg38-blacklist.v3.bed" |
||
| 453 | macs_gsize = [ |
||
| 454 | "50" : 2701262066, |
||
| 455 | "75" : 2749859687, |
||
| 456 | "100" : 2805665311, |
||
| 457 | "150" : 2862089864, |
||
| 458 | "200" : 2892537351 |
||
| 459 | ] |
||
| 460 | } |
||
| 461 | 'hg19' { |
||
| 462 | fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" |
||
| 463 | bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" |
||
| 464 | bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" |
||
| 465 | star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" |
||
| 466 | bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" |
||
| 467 | gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" |
||
| 468 | bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" |
||
| 469 | readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" |
||
| 470 | mito_name = "chrM" |
||
| 471 | blacklist = "${projectDir}/assets/blacklists/v1.0/hg19-blacklist.v1.bed" |
||
| 472 | macs_gsize = [ |
||
| 473 | "50" : 2684219875, |
||
| 474 | "75" : 2733035409, |
||
| 475 | "100" : 2774803719, |
||
| 476 | "150" : 2824648687, |
||
| 477 | "200" : 2848794782 |
||
| 478 | ] |
||
| 479 | } |
||
| 480 | 'mm10' { |
||
| 481 | fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" |
||
| 482 | bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" |
||
| 483 | bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" |
||
| 484 | star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" |
||
| 485 | bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" |
||
| 486 | gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" |
||
| 487 | bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" |
||
| 488 | readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" |
||
| 489 | mito_name = "chrM" |
||
| 490 | blacklist = "${projectDir}/assets/blacklists/v2.0/mm10-blacklist.v2.bed" |
||
| 491 | macs_gsize = [ |
||
| 492 | "50" : 2307679482, |
||
| 493 | "75" : 2406655830, |
||
| 494 | "100" : 2466184610, |
||
| 495 | "150" : 2492306232, |
||
| 496 | "200" : 2519386924 |
||
| 497 | ] |
||
| 498 | } |
||
| 499 | 'bosTau8' { |
||
| 500 | fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" |
||
| 501 | bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" |
||
| 502 | bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" |
||
| 503 | star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" |
||
| 504 | bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" |
||
| 505 | gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" |
||
| 506 | bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" |
||
| 507 | mito_name = "chrM" |
||
| 508 | macs_gsize = [ |
||
| 509 | "50" : 2370644326, |
||
| 510 | "75" : 2480511357, |
||
| 511 | "100" : 2567220492, |
||
| 512 | "150" : 2594494201, |
||
| 513 | "200" : 2648740387 |
||
| 514 | ] |
||
| 515 | } |
||
| 516 | 'ce10' { |
||
| 517 | fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" |
||
| 518 | bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" |
||
| 519 | bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" |
||
| 520 | star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" |
||
| 521 | bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" |
||
| 522 | gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" |
||
| 523 | bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" |
||
| 524 | readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" |
||
| 525 | mito_name = "chrM" |
||
| 526 | macs_gsize = [ |
||
| 527 | "50" : 95156190, |
||
| 528 | "75" : 96995949, |
||
| 529 | "100" : 98287299, |
||
| 530 | "150" : 98879728, |
||
| 531 | "200" : 98769409 |
||
| 532 | ] |
||
| 533 | } |
||
| 534 | 'canFam3' { |
||
| 535 | fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" |
||
| 536 | bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" |
||
| 537 | bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" |
||
| 538 | star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" |
||
| 539 | bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" |
||
| 540 | gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" |
||
| 541 | bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" |
||
| 542 | readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" |
||
| 543 | mito_name = "chrM" |
||
| 544 | macs_gsize = [ |
||
| 545 | "50" : 2237684358, |
||
| 546 | "75" : 2279860111, |
||
| 547 | "100" : 2293979635, |
||
| 548 | "150" : 2300527794, |
||
| 549 | "200" : 2313332891 |
||
| 550 | ] |
||
| 551 | } |
||
| 552 | 'danRer10' { |
||
| 553 | fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" |
||
| 554 | bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" |
||
| 555 | bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" |
||
| 556 | star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" |
||
| 557 | bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" |
||
| 558 | gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" |
||
| 559 | bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" |
||
| 560 | mito_name = "chrM" |
||
| 561 | macs_gsize = [ |
||
| 562 | "50" : 1172895610, |
||
| 563 | "75" : 1229400206, |
||
| 564 | "100" : 1253908756, |
||
| 565 | "150" : 1285330773, |
||
| 566 | "200" : 1292538906 |
||
| 567 | ] |
||
| 568 | } |
||
| 569 | 'dm6' { |
||
| 570 | fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" |
||
| 571 | bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" |
||
| 572 | bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" |
||
| 573 | star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" |
||
| 574 | bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" |
||
| 575 | gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" |
||
| 576 | bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" |
||
| 577 | mito_name = "chrM" |
||
| 578 | macs_gsize = [ |
||
| 579 | "50" : 123548253, |
||
| 580 | "75" : 124886264, |
||
| 581 | "100" : 126807034, |
||
| 582 | "150" : 126908682, |
||
| 583 | "200" : 128599061 |
||
| 584 | ] |
||
| 585 | } |
||
| 586 | 'equCab2' { |
||
| 587 | fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" |
||
| 588 | bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" |
||
| 589 | bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" |
||
| 590 | star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" |
||
| 591 | bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" |
||
| 592 | gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" |
||
| 593 | bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" |
||
| 594 | readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" |
||
| 595 | mito_name = "chrM" |
||
| 596 | macs_gsize = [ |
||
| 597 | "50" : 2294980416, |
||
| 598 | "75" : 2289244826, |
||
| 599 | "100" : 2334155865, |
||
| 600 | "150" : 2343297042, |
||
| 601 | "200" : 2350515523 |
||
| 602 | ] |
||
| 603 | } |
||
| 604 | 'galGal4' { |
||
| 605 | fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" |
||
| 606 | bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" |
||
| 607 | bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" |
||
| 608 | star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" |
||
| 609 | bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" |
||
| 610 | gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" |
||
| 611 | bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" |
||
| 612 | readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" |
||
| 613 | mito_name = "chrM" |
||
| 614 | macs_gsize = [ |
||
| 615 | "50" : 974987959, |
||
| 616 | "75" : 978772437, |
||
| 617 | "100" : 984935167, |
||
| 618 | "150" : 979442039, |
||
| 619 | "200" : 991678648 |
||
| 620 | ] |
||
| 621 | } |
||
| 622 | 'panTro4' { |
||
| 623 | fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" |
||
| 624 | bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" |
||
| 625 | bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" |
||
| 626 | star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" |
||
| 627 | bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" |
||
| 628 | gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" |
||
| 629 | bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" |
||
| 630 | readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" |
||
| 631 | mito_name = "chrM" |
||
| 632 | macs_gsize = [ |
||
| 633 | "50" : 2576111695, |
||
| 634 | "75" : 2702821987, |
||
| 635 | "100" : 2733435831, |
||
| 636 | "150" : 2735167196, |
||
| 637 | "200" : 2738912507 |
||
| 638 | ] |
||
| 639 | } |
||
| 640 | 'rn6' { |
||
| 641 | fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" |
||
| 642 | bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" |
||
| 643 | bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" |
||
| 644 | star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" |
||
| 645 | bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" |
||
| 646 | gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" |
||
| 647 | bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" |
||
| 648 | mito_name = "chrM" |
||
| 649 | macs_gsize = [ |
||
| 650 | "50" : 2375372135, |
||
| 651 | "75" : 2440746491, |
||
| 652 | "100" : 2480029900, |
||
| 653 | "150" : 2477334634, |
||
| 654 | "200" : 2478552171 |
||
| 655 | ] |
||
| 656 | } |
||
| 657 | 'sacCer3' { |
||
| 658 | fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" |
||
| 659 | bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" |
||
| 660 | bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" |
||
| 661 | star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" |
||
| 662 | bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" |
||
| 663 | readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" |
||
| 664 | mito_name = "chrM" |
||
| 665 | macs_gsize = [ |
||
| 666 | "50" : 11624332, |
||
| 667 | "75" : 11693438, |
||
| 668 | "100" : 11777680, |
||
| 669 | "150" : 11783749, |
||
| 670 | "200" : 11825681 |
||
| 671 | ] |
||
| 672 | } |
||
| 673 | 'susScr3' { |
||
| 674 | fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" |
||
| 675 | bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" |
||
| 676 | bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" |
||
| 677 | star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" |
||
| 678 | bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" |
||
| 679 | gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" |
||
| 680 | bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" |
||
| 681 | readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" |
||
| 682 | mito_name = "chrM" |
||
| 683 | macs_gsize = [ |
||
| 684 | "50" : 2105185708, |
||
| 685 | "75" : 2131615607, |
||
| 686 | "100" : 2149244400, |
||
| 687 | "150" : 2189757848, |
||
| 688 | "200" : 2203893315 |
||
| 689 | ] |
||
| 690 | } |
||
| 691 | } |
||
| 692 | } |