diff --git a/conf/czbiohub_aws_highpriority.config b/conf/czbiohub_aws_highpriority.config index 2bf9a4d..5ab796a 100644 --- a/conf/czbiohub_aws_highpriority.config +++ b/conf/czbiohub_aws_highpriority.config @@ -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 = "${params.transgenes_base}/zsGreen/zsGreen.gtf" - } - } } diff --git a/nfcore_custom.config b/nfcore_custom.config index de5961c..72dca30 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -17,7 +17,10 @@ profiles { cfc { includeConfig "${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" }