mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-22 16:29:55 +00:00
137 lines
4.9 KiB
Text
137 lines
4.9 KiB
Text
/*
|
|
* -------------------------------------------------
|
|
* Nextflow config file for Chan Zuckerberg Biohub
|
|
* -------------------------------------------------
|
|
* Defines reference genomes, using iGenome paths
|
|
* Imported under the default 'standard' Nextflow
|
|
* profile in nextflow.config
|
|
*/
|
|
|
|
//Profile config names for nf-core/configs
|
|
params {
|
|
config_profile_description = 'Chan Zuckerberg Biohub AWS Batch profile provided by nf-core/configs.'
|
|
config_profile_contact = 'Olga Botvinnik (@olgabot)'
|
|
config_profile_url = 'https://www.czbiohub.org/'
|
|
}
|
|
|
|
docker {
|
|
enabled = true
|
|
}
|
|
|
|
process {
|
|
executor = 'awsbatch'
|
|
queue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036'
|
|
errorStrategy = 'ignore'
|
|
}
|
|
|
|
workDir = "s3://czb-nextflow/intermediates/"
|
|
|
|
aws.region = 'us-west-2'
|
|
executor.awscli = '/home/ec2-user/miniconda/bin/aws'
|
|
params.tracedir = './'
|
|
|
|
params {
|
|
saveReference = true
|
|
|
|
// Largest SPOT instances available on AWS: https://ec2instances.info/
|
|
max_memory = 1952.GB
|
|
max_cpus = 96
|
|
max_time = 240.h
|
|
|
|
// Compatible with multiple versions of rnaseq pipeline
|
|
seq_center = "czbiohub"
|
|
seqCenter = "czbiohub"
|
|
|
|
// 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"
|
|
refseq_base = "s3://czbiohub-reference/ncbi/genomes/refseq/"
|
|
|
|
// AWS configurations
|
|
awsregion = "us-west-2"
|
|
awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036'
|
|
|
|
igenomes_ignore = true
|
|
igenomesIgnore = true //deprecated
|
|
|
|
fc_extra_attributes = 'gene_name'
|
|
fc_group_features = 'gene_id'
|
|
fc_group_features_type = 'gene_type'
|
|
|
|
trim_pattern = '_+S\\d+'
|
|
|
|
// GENCODE GTF and fasta files
|
|
genomes {
|
|
'GRCh38' {
|
|
fasta = "${params.gencode_base}/human/v30/GRCh38.p12.genome.ERCC92.fa"
|
|
gtf = "${params.gencode_base}/human/v30/gencode.v30.annotation.ERCC92.gtf"
|
|
transcript_fasta = "${params.gencode_base}/human/v30/gencode.v30.transcripts.ERCC92.fa"
|
|
star = "${params.gencode_base}/human/v30/STARIndex/"
|
|
salmon_index = "${params.gencode_base}/human/v30/salmon_index/"
|
|
}
|
|
'GRCm38' {
|
|
fasta = "${params.gencode_base}/mouse/vM21/GRCm38.p6.genome.ERCC92.fa"
|
|
gtf = "${params.gencode_base}/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf"
|
|
transcript_fasta = "${params.gencode_base}/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa"
|
|
star = "${params.gencode_base}/mouse/vM21/STARIndex/"
|
|
}
|
|
'AaegL5.0' {
|
|
fasta = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna"
|
|
gtf = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf"
|
|
bed = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed"
|
|
star = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/"
|
|
}
|
|
}
|
|
|
|
transgenes {
|
|
'ChR2' {
|
|
fasta = "${params.transgenes_base}/ChR2/ChR2.fa"
|
|
gtf = "${params.transgenes_base}/ChR2/ChR2.gtf"
|
|
}
|
|
'Cre' {
|
|
fasta = "${params.transgenes_base}/Cre/Cre.fa"
|
|
gtf = "${params.transgenes_base}/Cre/Cre.gtf"
|
|
}
|
|
'ERCC' {
|
|
fasta = "${params.transgenes_base}/ERCC92/ERCC92.fa"
|
|
gtf = "${params.transgenes_base}/ERCC92/ERCC92.gtf"
|
|
}
|
|
'GCaMP6m' {
|
|
fasta = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa"
|
|
gtf = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf"
|
|
}
|
|
'GFP' {
|
|
fasta = "${params.transgenes_base}/Gfp/Gfp.fa"
|
|
gtf = "${params.transgenes_base}/Gfp/Gfp.gtf"
|
|
}
|
|
'NpHR' {
|
|
fasta = "${params.transgenes_base}/NpHR/NpHR.fa"
|
|
gtf = "${params.transgenes_base}/NpHR/NpHR.gtf"
|
|
}
|
|
'RCaMP' {
|
|
fasta = "${params.transgenes_base}/RCaMP/RCaMP.fa"
|
|
gtf = "${params.transgenes_base}/RCaMP/RCaMP.gtf"
|
|
}
|
|
'RGECO' {
|
|
fasta = "${params.transgenes_base}/RGECO/RGECO.fa"
|
|
gtf = "${params.transgenes_base}/RGECO/RGECO.gtf"
|
|
}
|
|
'Tdtom' {
|
|
fasta = "${params.transgenes_base}/Tdtom/Tdtom.fa"
|
|
gtf = "${params.transgenes_base}/Tdtom/Tdtom.gtf"
|
|
}
|
|
'Car-T' {
|
|
fasta = "${params.transgenes_base}/car-t/car-t.fa"
|
|
gtf = "${params.transgenes_base}/car-t/car-t.gtf"
|
|
}
|
|
'zsGreen' {
|
|
fasta = "${params.transgenes_base}/zsGreen/zsGreen.fa"
|
|
gtf = "${params.transgenes_base}/zsGreen/zsGreen.gtf"
|
|
}
|
|
}
|
|
}
|