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Initial commit of CZBiohub

This commit is contained in:
Olga Botvinnik 2019-05-30 11:15:38 -07:00
parent 441ddbcdab
commit 66eeeebe81

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conf/czbiohub.config Normal file
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/*
* -------------------------------------------------
* Nextflow config file for UPPMAX (milou / irma)
* -------------------------------------------------
* Defines reference genomes, using iGenome paths
* Imported under the default 'standard' Nextflow
* profile in nextflow.config
*/
docker {
enabled = true
}
process {
executor = 'awsbatch'
}
params {
saveReference = true
// Largest SPOT instances available on AWS: https://ec2instances.info/
max_memory = 1952.GB
max_cpus = 96
max_time = 240.h
// illumina iGenomes reference file paths on CZ Biohub reference s3 bucket
// No final slash because it's added later
igenomes_base = "s3://czbiohub-reference/igenomes"
// GENCODE (human + mouse) reference file paths on CZ Biohub reference s3 bucket
// No final slash because it's added later
gencode_base = "s3://czbiohub-reference/gencode"
transgenes_base = "s3://czbiohub-reference/transgenes"
// AWS configurations
awsregion = "us-west-2"
awsqueue = "nextflow"
workDir = "s3://czb-nextflow/rnaseq/"
// GENCODE GTF and fasta files
genomes {
'GRCh38' {
fasta = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa.gz"
gtf = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf.gz"
}
'GRCm38' {
fasta = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa.gz"
gtf = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf.gz"
}
}
transgenes {
'ChR2' {
fasta = "${params.transgenes_base}/ChR2/ChR2.fa.gz"
gtf = "${params.transgenes_base}/ChR2/ChR2.gtf.gz"
}
'Cre' {
fasta = "${params.transgenes_base}/Cre/Cre.fa.gz"
gtf = "${params.transgenes_base}/Cre/Cre.gtf.gz"
}
'ERCC' {
fasta = "${params.transgenes_base}/ERCC92/ERCC92.fa.gz"
gtf = "${params.transgenes_base}/ERCC92/ERCC92.gtf.gz"
}
'GCaMP6m' {
fasta = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa.gz"
gtf = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf.gz"
}
'GFP' {
fasta = "${params.transgenes_base}/Gfp/Gfp.fa.gz"
gtf = "${params.transgenes_base}/Gfp/Gfp.gtf.gz"
}
'NpHR' {
fasta = "${params.transgenes_base}/NpHR/NpHR.fa.gz"
gtf = "${params.transgenes_base}/NpHR/NpHR.gtf.gz"
}
'RCaMP' {
fasta = "${params.transgenes_base}/RCaMP/RCaMP.fa.gz"
gtf = "${params.transgenes_base}/RCaMP/RCaMP.gtf.gz"
}
'RGECO' {
fasta = "${params.transgenes_base}/RGECO/RGECO.fa.gz"
gtf = "${params.transgenes_base}/RGECO/RGECO.gtf.gz"
}
'Tdtom' {
fasta = "${params.transgenes_base}/Tdtom/Tdtom.fa.gz"
gtf = "${params.transgenes_base}/Tdtom/Tdtom.gtf.gz"
}
'Car-T' {
fasta = "${params.transgenes_base}/car-t/car-t.fa.gz"
gtf = "${params.transgenes_base}/car-t/car-t.gtf.gz"
}
'zsGreen' {
fasta = "${params.transgenes_base}/zsGreen/zsGreen.fa.gz"
gtf = "${params.transgenes_base}/zsGreen/zsGreen.gtf.gz"
}
}
}