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