From 93c4ba67a01122d702c5b73d3d8d1c7c3a54de56 Mon Sep 17 00:00:00 2001
From: kalayaneech <kalayanee.chai@mail.kmutt.ac.th>
Date: Thu, 25 Aug 2022 16:17:09 +0700
Subject: [PATCH] adding adcra configuration

---
 conf/adcra.config    | 40 ++++++++++++++++++++++++++++++++++++++++
 docs/adcra.md        | 29 +++++++++++++++++++++++++++++
 nfcore_custom.config |  1 +
 3 files changed, 70 insertions(+)
 create mode 100644 conf/adcra.config
 create mode 100644 docs/adcra.md

diff --git a/conf/adcra.config b/conf/adcra.config
new file mode 100644
index 0000000..0654c5a
--- /dev/null
+++ b/conf/adcra.config
@@ -0,0 +1,40 @@
+/*
+* --------------------------------------------------------------
+*   nf-core pipelines config file for AD project using CRA HPC
+* --------------------------------------------------------------
+*/
+
+params {
+  config_profile_name = 'adcra'
+  config_profile_description = 'CRA HPC profile provided by nf-core/configs'
+  config_profile_contact = 'Kalayanee Chairat (@kalayaneech)'
+  config_profile_url = 'https://bioinformatics.kmutt.ac.th/'
+  }
+  
+params {  
+  max_cpus = 16
+  max_memory = 128.GB
+  max_time = 120.h
+}
+
+// Specify the job scheduler
+executor {  
+  name = 'slurm'
+  queueSize = 20
+  submitRateLimit = '6/1min'
+}
+
+Singularity {
+  enabled = true
+  autoMounts = true
+}
+
+process {
+  scratch = true
+  queue = 'unlimit'
+  queueStatInterval = '10 min'
+  maxRetries = 3
+  errorStrategy = { task.attempt <=3 ? 'retry' : 'finish' }
+  cache = 'lenient'
+  exitStatusReadTimeoutMillis = '2700000'
+}
diff --git a/docs/adcra.md b/docs/adcra.md
new file mode 100644
index 0000000..5e9d058
--- /dev/null
+++ b/docs/adcra.md
@@ -0,0 +1,29 @@
+# nf-core/configs: CRA HPC Configuration
+nfcore pipeline sarek and rnaseq have been tested on the CRA HPC.
+
+## Before running the pipeline
+- You will need an account to use the CRA HPC cluster in order to run the pipeline.
+- Make sure that Singularity and Nextflow are installed.
+- Downlode pipeline singularity images to a HPC system using [nf-core tools](https://nf-co.re/tools/#downloading-pipelines-for-offline-use)
+```
+$ conda install nf-core
+$ nf-core download
+```
+- You will need to specify a Singularity cache directory in your ~./bashrc. This will store your container images in this cache directory without repeatedly downloading them every time you run a pipeline. Since space on home directory is limited, using lustre file system is recommended. 
+```
+export NXF_SINGULARITY_CACHEDIR = "/lustre/fs0/storage/yourCRAAccount/cache_dir"
+```
+- Download iGenome reference to be used as a local copy.
+```
+$ aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/ /lustre/fs0/storage/yourCRAAccount/references/Homo_sapiens/GATK/GRCh38/
+```
+## Running the pipeline using the adcra config profile
+- Run the pipeline within a [screen](https://linuxize.com/post/how-to-use-linux-screen/) or [tmux](https://linuxize.com/post/getting-started-with-tmux/) session.
+- Specify the config profile with ```-profile adcra```.
+- Using lustre file systems to store results (```--outdir```) and intermediate files (```-work-dir```) is recommended.
+```
+nextflow run /path/to/nf-core/<pipeline-name> -profile adcra \
+--genome GRCh38 \
+--igenomes_base /path/to/genome_references/ \
+... # the rest of pipeline flags
+```
diff --git a/nfcore_custom.config b/nfcore_custom.config
index 6f0ac6c..0083bc5 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -11,6 +11,7 @@
 //Please use a new line per include Config section to allow easier linting/parsing. Thank you.
 profiles {
   abims        { includeConfig "${params.custom_config_base}/conf/abims.config" }
+  adcra        { includeConfig "${params.custom_config_base}/conf/adcra.config" }
   alice        { includeConfig "${params.custom_config_base}/conf/alice.config" }
   aws_tower    { includeConfig "${params.custom_config_base}/conf/aws_tower.config" }
   awsbatch     { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }