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Use flat nongzipped files

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This commit is contained in:
Olga Botvinnik 2019-05-31 13:17:48 -07:00
parent 1b2fcf5a98
commit 9c0315addb
1 changed files with 26 additions and 26 deletions
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52
conf/czbiohub.config
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@ -47,59 +47,59 @@ params {
// GENCODE GTF and fasta files // GENCODE GTF and fasta files
genomes { genomes {
'GRCh38' { 'GRCh38' {
fasta = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa.gz" fasta = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa"
gtf = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf.gz" gtf = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf"
} }
'GRCm38' { 'GRCm38' {
fasta = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa.gz" fasta = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa"
gtf = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf.gz" gtf = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf"
} }
} }
transgenes { transgenes {
'ChR2' { 'ChR2' {
fasta = "${params.transgenes_base}/ChR2/ChR2.fa.gz" fasta = "${params.transgenes_base}/ChR2/ChR2.fa"
gtf = "${params.transgenes_base}/ChR2/ChR2.gtf.gz" gtf = "${params.transgenes_base}/ChR2/ChR2.gtf"
} }
'Cre' { 'Cre' {
fasta = "${params.transgenes_base}/Cre/Cre.fa.gz" fasta = "${params.transgenes_base}/Cre/Cre.fa"
gtf = "${params.transgenes_base}/Cre/Cre.gtf.gz" gtf = "${params.transgenes_base}/Cre/Cre.gtf"
} }
'ERCC' { 'ERCC' {
fasta = "${params.transgenes_base}/ERCC92/ERCC92.fa.gz" fasta = "${params.transgenes_base}/ERCC92/ERCC92.fa"
gtf = "${params.transgenes_base}/ERCC92/ERCC92.gtf.gz" gtf = "${params.transgenes_base}/ERCC92/ERCC92.gtf"
} }
'GCaMP6m' { 'GCaMP6m' {
fasta = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa.gz" fasta = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa"
gtf = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf.gz" gtf = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf"
} }
'GFP' { 'GFP' {
fasta = "${params.transgenes_base}/Gfp/Gfp.fa.gz" fasta = "${params.transgenes_base}/Gfp/Gfp.fa"
gtf = "${params.transgenes_base}/Gfp/Gfp.gtf.gz" gtf = "${params.transgenes_base}/Gfp/Gfp.gtf"
} }
'NpHR' { 'NpHR' {
fasta = "${params.transgenes_base}/NpHR/NpHR.fa.gz" fasta = "${params.transgenes_base}/NpHR/NpHR.fa"
gtf = "${params.transgenes_base}/NpHR/NpHR.gtf.gz" gtf = "${params.transgenes_base}/NpHR/NpHR.gtf"
} }
'RCaMP' { 'RCaMP' {
fasta = "${params.transgenes_base}/RCaMP/RCaMP.fa.gz" fasta = "${params.transgenes_base}/RCaMP/RCaMP.fa"
gtf = "${params.transgenes_base}/RCaMP/RCaMP.gtf.gz" gtf = "${params.transgenes_base}/RCaMP/RCaMP.gtf"
} }
'RGECO' { 'RGECO' {
fasta = "${params.transgenes_base}/RGECO/RGECO.fa.gz" fasta = "${params.transgenes_base}/RGECO/RGECO.fa"
gtf = "${params.transgenes_base}/RGECO/RGECO.gtf.gz" gtf = "${params.transgenes_base}/RGECO/RGECO.gtf"
} }
'Tdtom' { 'Tdtom' {
fasta = "${params.transgenes_base}/Tdtom/Tdtom.fa.gz" fasta = "${params.transgenes_base}/Tdtom/Tdtom.fa"
gtf = "${params.transgenes_base}/Tdtom/Tdtom.gtf.gz" gtf = "${params.transgenes_base}/Tdtom/Tdtom.gtf"
} }
'Car-T' { 'Car-T' {
fasta = "${params.transgenes_base}/car-t/car-t.fa.gz" fasta = "${params.transgenes_base}/car-t/car-t.fa"
gtf = "${params.transgenes_base}/car-t/car-t.gtf.gz" gtf = "${params.transgenes_base}/car-t/car-t.gtf"
} }
'zsGreen' { 'zsGreen' {
fasta = "${params.transgenes_base}/zsGreen/zsGreen.fa.gz" fasta = "${params.transgenes_base}/zsGreen/zsGreen.fa"
gtf = "${params.transgenes_base}/zsGreen/zsGreen.gtf.gz" gtf = "${params.transgenes_base}/zsGreen/zsGreen.gtf"
} }
} }
} }