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