From 0cabf67b6193f162bd907765021594cb6acbd396 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.miller@elembio.com>
Date: Tue, 4 Oct 2022 15:09:56 -0500
Subject: [PATCH 1/2] feat(demultiplex): Add optimized transfers for
 bases2fastq

---
 conf/pipeline/demultiplex/aws_tower.config | 29 ++++++++++++++++++++++
 pipeline/demultiplex.config                | 13 ++++++++++
 2 files changed, 42 insertions(+)
 create mode 100644 conf/pipeline/demultiplex/aws_tower.config
 create mode 100644 pipeline/demultiplex.config

diff --git a/conf/pipeline/demultiplex/aws_tower.config b/conf/pipeline/demultiplex/aws_tower.config
new file mode 100644
index 0000000..520487f
--- /dev/null
+++ b/conf/pipeline/demultiplex/aws_tower.config
@@ -0,0 +1,29 @@
+// Profile config names for nf-core/configs
+
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'Edmund Miller(@emiller88)'
+  config_profile_description = 'nf-core/demultiplex AWS Tower profile provided by nf-core/configs'
+}
+
+aws {
+   batch {
+      maxParallelTransfers = 24
+      maxTransferAttempts = 3
+   }
+   client {
+      maxConnections = 24
+      uploadMaxThreads = 24
+      maxErrorRetry = 3
+      socketTimeout = 3600000
+      uploadRetrySleep = 1000
+      uploadChunkSize = 32.MB
+   }
+}
+
+process {
+    withName: BASES2FASTQ {
+        cpus = 16
+        memory = 48.GB
+    }
+}
diff --git a/pipeline/demultiplex.config b/pipeline/demultiplex.config
new file mode 100644
index 0000000..46c3e08
--- /dev/null
+++ b/pipeline/demultiplex.config
@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/demultiplex custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/demultiplex folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  aws_tower { includeConfig "${params.custom_config_base}/conf/pipeline/demultiplex/aws_tower.config" }
+}

From 33708acdc58a91f38f62b0b1fe0f3e372e57bf2a Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.miller@elembio.com>
Date: Tue, 4 Oct 2022 15:22:26 -0500
Subject: [PATCH 2/2] docs(demultiplex): Add aws_tower docs

---
 README.md                              |  2 ++
 docs/pipeline/demultiplex/aws_tower.md | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+)
 create mode 100644 docs/pipeline/demultiplex/aws_tower.md

diff --git a/README.md b/README.md
index ddf9267..50c34aa 100644
--- a/README.md
+++ b/README.md
@@ -206,6 +206,8 @@ Currently documentation is available for the following pipelines within specific
   - [SBC_SHARC](docs/pipeline/atacseq/sbc_sharc.md)
 - chipseq
   - [SBC_SHARC](docs/pipeline/chipseq/sbc_sharc.md)
+- demultiplex
+  - [AWS_TOWER](docs/pipeline/demultiplex/aws_tower.md)
 - eager
   - [EVA](docs/pipeline/eager/eva.md)
 - mag
diff --git a/docs/pipeline/demultiplex/aws_tower.md b/docs/pipeline/demultiplex/aws_tower.md
new file mode 100644
index 0000000..eb87186
--- /dev/null
+++ b/docs/pipeline/demultiplex/aws_tower.md
@@ -0,0 +1,19 @@
+# nf-core/configs: AWS Tower Demultiplex specific configuration
+
+Extra specific configuration for demultiplex pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile aws_tower`.
+
+This will download and launch the demultiplex specific [`aws_tower.config`](../../../conf/pipeline/demultiplex/aws_tower.config) which has been pre-configured with a setup suitable for AWS batch through tower.
+
+Example: `nextflow run nf-core/demultiplex -profile aws_tower`
+
+## eager specific configurations for eva
+
+Specific configurations for AWS has been made for demultiplex.
+
+### General profiles
+
+- The general AWS Tower profile runs with default nf-core/demultiplex parameters, but with modifications to account file transfer speed and optimized bases2fastq resources.