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Make czbiohub_aws_highpriority only set the AWS Batch queue and nothing else

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This commit is contained in:
Olga Botvinnik 2019-07-03 16:01:47 -07:00
parent 917ec0863d
commit 069963ff8a
2 changed files with 4 additions and 116 deletions
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115
conf/czbiohub_aws_highpriority.config
View file

@ -7,121 +7,6 @@
* 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 = 'highpriority-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"
// AWS configurations
awsregion = "us-west-2"
awsqueue = "nextflow"
igenomesIgnore = true
fc_extra_attributes = 'gene_name'
fc_group_features = 'gene_id'
fc_group_features_type = 'gene_type'
// 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"
start = "${params.gencode_base}/mouse/vM21/STARIndex/"
}
}
transgenes {
'ChR2' {
fasta = "${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"
}
}
}

5
nfcore_custom.config
View file

@ -17,7 +17,10 @@ profiles {
cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
czbiohub_aws_highpriority {
includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"
includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"
}
gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
mendel { includeConfig "${params.custom_config_base}/conf/mendel.config" }