From 8aefa66cf190ba0cf7db23f499e938a424d51651 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Wed, 28 Feb 2024 17:18:02 +1300
Subject: [PATCH] Added pfr profile and params

---
 pfr/params.json    |  0
 pfr/profile.config | 12 ++++++++++++
 pfr_assemblyqc     | 24 ++++++++++++++++++++++++
 3 files changed, 36 insertions(+)
 create mode 100644 pfr/params.json
 create mode 100644 pfr/profile.config
 create mode 100644 pfr_assemblyqc

diff --git a/pfr/params.json b/pfr/params.json
new file mode 100644
index 0000000..e69de29
diff --git a/pfr/profile.config b/pfr/profile.config
new file mode 100644
index 0000000..f219d13
--- /dev/null
+++ b/pfr/profile.config
@@ -0,0 +1,12 @@
+profiles {
+    pfr {
+        process {
+            executor        = 'slurm'
+        }
+
+        apptainer {
+            envWhitelist    = "APPTAINER_BINDPATH,APPTAINER_BIND"
+            cacheDir        = "/workspace/assemblyqc/singularity"
+        }
+    }
+}
diff --git a/pfr_assemblyqc b/pfr_assemblyqc
new file mode 100644
index 0000000..4f23a41
--- /dev/null
+++ b/pfr_assemblyqc
@@ -0,0 +1,24 @@
+#!/bin/bash -e
+
+#SBATCH --job-name ASMQC
+#SBATCH --time=7-00:00:00
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --output pfr_assemblyqc.stdout
+#SBATCH --error pfr_assemblyqc.stderr
+#SBATCH --mem=4G
+
+ml unload perl
+ml apptainer/1.1
+ml nextflow/23.04.4
+
+export TMPDIR="/workspace/$USER/tmp"
+export APPTAINER_BINDPATH="$APPTAINER_BINDPATH,$TMPDIR:$TMPDIR,$TMPDIR:/tmp"
+
+nextflow \
+    main.nf \
+    -c pfr/profile.config \
+    -profile pfr,apptainer \
+    -resume \
+    --params-file pfr/params.json