Make czbiohub_aws_highpriority only set the AWS Batch queue and nothing else

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"
-    }
-  }
 }

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" }