From c8a53f6cbde33eaf366571d967ab3c49fc5ab405 Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Fri, 11 Oct 2024 15:25:47 -0400
Subject: [PATCH] add app devops guidelines

---
 docs/devops.md    | 13 +++++++++++++
 docs/pipelines.md | 26 +++++++++++++++++++++++++-
 2 files changed, 38 insertions(+), 1 deletion(-)

diff --git a/docs/devops.md b/docs/devops.md
index 5333975..2957f21 100644
--- a/docs/devops.md
+++ b/docs/devops.md
@@ -2,6 +2,19 @@
 
 Content ![](https://img.shields.io/badge/status-WorkInProgress-yellow)
 
+## App development
+
+- Use HBC or bcbio organization
+- Private repo prior to release
+- Test data needs to be part of the code
+- README to explain how to use the test data
+- First release should be prior to client
+    - Must be usable at First release
+    - At least one other person to review and approve 
+    - After that main branch get blocked and version numbers start at 1.0.0
+    - Then start dev branch
+- Each time we merge a Pull request, we need to make a release
+- Publish on Posit connect with a new name that matches the version
 
 ## Data management
 
diff --git a/docs/pipelines.md b/docs/pipelines.md
index a354d24..c45c90c 100644
--- a/docs/pipelines.md
+++ b/docs/pipelines.md
@@ -1,6 +1,6 @@
 # Introduction to HCBC pipelines
 
-Content ![](https://img.shields.io/badge/status-WorkInProgress-yellow)
+Content - ![](https://img.shields.io/badge/status-WorkInProgress-yellow)
 
 ## Nextflow in Seqera platform
 
@@ -32,6 +32,30 @@ You can add more columns to this file with more metadata, and use this file as t
 
 ## Nextflow in O2
 
+Nextflow is available at `/n/app/bcbio/nextflow/nextflow`. 
+Singularity containers at available at `/n/app/singularity/containers/shared/bcbio/`.
+
+An example of batch script is:
+
+```
+#!/bin/bash
+
+#SBATCH --job-name=Nextflow      # Job name
+#SBATCH --partition=priority            # Partition name
+#SBATCH --time=1-23:59                 # Runtime in D-HH:MM format
+#SBATCH --nodes=1                      # Number of nodes (keep at 1)
+#SBATCH --ntasks=1                     # Number of tasks per node (keep at 1)
+#SBATCH --cpus-per-task=8            # CPU cores requested per task (change for threaded jobs)
+#SBATCH --mem=128G                     # Memory needed per node (total)
+#SBATCH --error=jobid_%j.err           # File to which STDERR will be written, including job ID
+#SBATCH --output=jobid_%j.out          # File to which STDOUT will be written, including job ID
+#SBATCH --mail-type=ALL                # Type of email notification (BEGIN, END, FAIL, ALL)
+
+module load java/jdk-21.0.2
+export NXF_APPTAINER_CACHEDIR=/n/app/singularity/containers/shared/bcbio/nf-core-rnaseq-3.14.0
+export NXF_SINGULARITY_LIBRARYDIR=/n/app/singularity/containers/shared/bcbio/nf-core-rnaseq-3.14.0
+```
+
 ### RNAseq
 
 Example of running in single node Nextflow/nf-core/rnaseq in O2.