1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-12-23 10:58:16 +00:00
nf-configs/conf/czbiohub_aws.config
2021-05-19 13:36:15 -07:00

146 lines
5 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'
aws.batch.cliPath = '/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"
}
}
}
profiles {
highpriority {
process {
queue = 'highpriority-971039e0-830c-11e9-9e0b-02c5b84a8036'
}
}
}