From 66eeeebe81d1aef1d8083e492484e47975d8760b Mon Sep 17 00:00:00 2001
From: Olga Botvinnik <olga.botvinnik@gmail.com>
Date: Thu, 30 May 2019 11:15:38 -0700
Subject: [PATCH] Initial commit of CZBiohub

---
 conf/czbiohub.config | 98 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 98 insertions(+)
 create mode 100644 conf/czbiohub.config

diff --git a/conf/czbiohub.config b/conf/czbiohub.config
new file mode 100644
index 0000000..ff1523e
--- /dev/null
+++ b/conf/czbiohub.config
@@ -0,0 +1,98 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for UPPMAX (milou / irma)
+ * -------------------------------------------------
+ * Defines reference genomes, using iGenome paths
+ * Imported under the default 'standard' Nextflow
+ * profile in nextflow.config
+ */
+
+docker {
+  enabled = true
+}
+
+process {
+  executor = 'awsbatch'
+}
+
+params {
+  saveReference = true
+
+  // Largest SPOT instances available on AWS: https://ec2instances.info/
+  max_memory = 1952.GB
+  max_cpus = 96
+  max_time = 240.h
+
+  // 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"
+  workDir = "s3://czb-nextflow/rnaseq/"
+
+  // GENCODE GTF and fasta files
+  genomes {
+    'GRCh38' {
+      fasta   = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa.gz"
+      gtf     = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf.gz"
+    }
+    'GRCm38' {
+      fasta   = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa.gz"
+      gtf     = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf.gz"
+    }
+  }
+
+  transgenes {
+    'ChR2' {
+      fasta   = "${params.transgenes_base}/ChR2/ChR2.fa.gz"
+      gtf     = "${params.transgenes_base}/ChR2/ChR2.gtf.gz"
+    }
+    'Cre' {
+      fasta   = "${params.transgenes_base}/Cre/Cre.fa.gz"
+      gtf     = "${params.transgenes_base}/Cre/Cre.gtf.gz"
+    }
+    'ERCC' {
+      fasta   = "${params.transgenes_base}/ERCC92/ERCC92.fa.gz"
+      gtf     = "${params.transgenes_base}/ERCC92/ERCC92.gtf.gz"
+    }
+    'GCaMP6m' {
+      fasta   = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa.gz"
+      gtf     = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf.gz"
+    }
+    'GFP' {
+      fasta   = "${params.transgenes_base}/Gfp/Gfp.fa.gz"
+      gtf     = "${params.transgenes_base}/Gfp/Gfp.gtf.gz"
+    }
+    'NpHR' {
+      fasta   = "${params.transgenes_base}/NpHR/NpHR.fa.gz"
+      gtf     = "${params.transgenes_base}/NpHR/NpHR.gtf.gz"
+    }
+    'RCaMP' {
+      fasta   = "${params.transgenes_base}/RCaMP/RCaMP.fa.gz"
+      gtf     = "${params.transgenes_base}/RCaMP/RCaMP.gtf.gz"
+    }
+    'RGECO' {
+      fasta   = "${params.transgenes_base}/RGECO/RGECO.fa.gz"
+      gtf     = "${params.transgenes_base}/RGECO/RGECO.gtf.gz"
+    }
+    'Tdtom' {
+      fasta   = "${params.transgenes_base}/Tdtom/Tdtom.fa.gz"
+      gtf     = "${params.transgenes_base}/Tdtom/Tdtom.gtf.gz"
+    }
+    'Car-T' {
+      fasta   = "${params.transgenes_base}/car-t/car-t.fa.gz"
+      gtf     = "${params.transgenes_base}/car-t/car-t.gtf.gz"
+    }
+    'zsGreen' {
+      fasta   = "${params.transgenes_base}/zsGreen/zsGreen.fa.gz"
+      gtf     = "${params.transgenes_base}/zsGreen/zsGreen.gtf.gz"
+    }
+  }
+}