From 69d1a14894146ed5781f4c487327d08815d4bd5e Mon Sep 17 00:00:00 2001
From: Alex Rajewski <rajewski23@gmail.com>
Date: Fri, 22 Apr 2022 10:17:13 -0700
Subject: [PATCH 1/5] basic Cedars-Sinai HPC config file

---
 conf/cedars.config | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 conf/cedars.config

diff --git a/conf/cedars.config b/conf/cedars.config
new file mode 100644
index 0000000..d9b9027
--- /dev/null
+++ b/conf/cedars.config
@@ -0,0 +1,26 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Cedars-Sinai Medical Center HPC Profile'
+  config_profile_contact = 'Alex Rajewski (@rajewski)'
+  config_profile_url = 'https://www.cedars-sinai.edu/research/cores/informatics-computing/resources.html'
+  max_memory = 90.GB
+  max_cpus = 10
+  max_time = 240.h
+}
+
+// Specify the queing system
+executor {
+  name = "sge"
+}
+
+process {
+  penv = 'smp'
+  beforeScript =
+  """
+  module load 'singularity/3.6.0'
+  """
+}
+
+singularity {
+  enabled = true
+}

From 766eb450be7775798f33dca4be1ef59f8dbcb84d Mon Sep 17 00:00:00 2001
From: Alex Rajewski <rajewski23@gmail.com>
Date: Fri, 22 Apr 2022 10:23:19 -0700
Subject: [PATCH 2/5] usage notes

---
 docs/cedars.md | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 docs/cedars.md

diff --git a/docs/cedars.md b/docs/cedars.md
new file mode 100644
index 0000000..ba09eb1
--- /dev/null
+++ b/docs/cedars.md
@@ -0,0 +1,7 @@
+# Cedars-Sinai Medical Center HPC
+
+  - You will need HPC access from EIS, which can be requested in the Service Center.
+  - You will need to load the nextflow module on the HPC before running any pipelines (`module load nextflow`). This should automatically load Java as well.
+  - Run this with `-profile cedars`
+  - By default this config file does not specify a queue for submission, and things will thus go to `all.q`. Because of that, the memory and cpu limits have been set accordingly.
+  - We  highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`

From c60d73b56594786ef983f86f8bc8396befbbb611 Mon Sep 17 00:00:00 2001
From: Alex Rajewski <rajewski23@gmail.com>
Date: Fri, 22 Apr 2022 10:26:32 -0700
Subject: [PATCH 3/5] add Cedars-Sinai HPC

---
 nfcore_custom.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nfcore_custom.config b/nfcore_custom.config
index 9b088b1..939fd3a 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -24,6 +24,7 @@ profiles {
   cbe          { includeConfig "${params.custom_config_base}/conf/cbe.config" }
   ccga_dx      { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
   ccga_med     { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
+  cedars       { includeConfig "${params.custom_config_base}/conf/cedars.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
   cfc_dev      { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" }
   cheaha       { includeConfig "${params.custom_config_base}/conf/cheaha.config" }

From aa2c3e256b28b371c1115ac9413508499fd71088 Mon Sep 17 00:00:00 2001
From: Alex Rajewski <rajewski23@gmail.com>
Date: Fri, 22 Apr 2022 10:27:50 -0700
Subject: [PATCH 4/5] add cedars-sinai

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 55fa3b9..398acca 100644
--- a/README.md
+++ b/README.md
@@ -99,6 +99,7 @@ Currently documentation is available for the following systems:
 - [CBE](docs/cbe.md)
 - [CCGA_DX](docs/ccga_dx.md)
 - [CCGA_MED](docs/ccga_med.md)
+- [Cedars-Sinai](docs/cedars.md)
 - [CFC](docs/cfc.md)
 - [CHEAHA](docs/cheaha.md)
 - [Computerome](docs/computerome.md)

From d261b3df7896cb791473d0b53f8e1a868f61e472 Mon Sep 17 00:00:00 2001
From: Alex Rajewski <rajewski23@gmail.com>
Date: Fri, 22 Apr 2022 10:29:22 -0700
Subject: [PATCH 5/5] add cedars-sinai

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 38ddb4f..3abcba6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -43,6 +43,7 @@ jobs:
           - "cbe"
           - "ccga_dx"
           - "ccga_med"
+          - "cedars"
           - "cfc"
           - "cfc_dev"
           - "cheaha"