From 0f07af91d1c011d91754d27b8da26a0538ebda84 Mon Sep 17 00:00:00 2001
From: ucbtrm5 <ucbtrm5@login12.myriad.ucl.ac.uk>
Date: Wed, 1 Apr 2026 10:44:27 +0100
Subject: [PATCH] Fix HiTE arguments for v3.3.3 and adjusted hite resources on 
 Myriad HPC config

---
 modules/local/hite.nf |  9 +++++----
 ucl_myriad.config     | 37 +++++++++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 4 deletions(-)
 create mode 100644 ucl_myriad.config

diff --git a/modules/local/hite.nf b/modules/local/hite.nf
index ba9f35f..30c92c5 100644
--- a/modules/local/hite.nf
+++ b/modules/local/hite.nf
@@ -2,7 +2,7 @@ process HITE {
     label 'process_single'
     label 'process_long'
     tag "$species"
-    container = 'kanghu/hite:3.2.0'
+    container = 'kanghu/hite:3.3.3'
     stageInMode = 'copy'
     
     input:
@@ -34,14 +34,15 @@ process HITE {
     cd /HiTE
 
 
-    python main.py --genome \${newpath} --outdir \${mydir}/${species}_hite_results --thread ${task.cpus}
+    python main.py --work_dir \${mydir} --genome \${newpath} --out_dir \${mydir}/${species}_hite_results --thread ${task.cpus} --annotate 1 --plant 0
 
     cd \${mydir}/${species}_hite_results/
 
-    cat <<-END_VERSIONS > versions.yml
+    cat <<-END_VERSIONS > \${mydir}/versions.yml
+
     "${task.process}":
        Python version: \$(python --version | cut -f 2 -d " ")
-        HiTE version: 3.2.0
+        HiTE version: 3.3.3
        Repeat Masker version: \$(RepeatMasker | grep version | cut -f 3 -d " ")
        Repeat Modeler version: \$(RepeatModeler | grep /opt/conda/envs/HiTE/share/RepeatModeler/RepeatModeler | cut -f 3 -d " ")
         LTRPipeline version: \$(LTRPipeline -version)
diff --git a/ucl_myriad.config b/ucl_myriad.config
new file mode 100644
index 0000000..4208bb3
--- /dev/null
+++ b/ucl_myriad.config
@@ -0,0 +1,37 @@
+params {
+    config_profile_description = 'University College London Myriad cluster'
+    config_profile_contact     = 'Chris Wyatt (ucbtcdr@ucl.ac.uk), Fernando Duarte (f.frutos@ucl.ac.uk)'
+    config_profile_url         = 'https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/'
+}
+
+executor {
+    name = 'sge'
+    queueSize = 100 // Limit number of jobs sent to qsub (max is 1000, but in case user submits more than one job)
+    submitRateLimit = '10/1s'  // Submit max 10 jobs per second. To ease pressure on scheduler.
+}
+
+process {
+    penv           = 'smp'
+    clusterOptions = {
+        def mem = task.memory.mega
+        def cpus = task.cpus
+        def memoryPerCpu = mem / task.cpus // We need memory per cpu, as is not possible to request memory per job
+        def baseOpts = "-S /bin/bash -l mem=${memoryPerCpu}M "
+        return baseOpts
+    }
+    scratch = false
+}
+
+singularity {
+    enabled    = true
+    autoMounts = true
+    cacheDir   = "${System.getenv('HOME')}/Scratch/.apptainer/pull"
+    runOptions = "-B ${System.getenv('HOME')},${System.getenv('PWD')} --no-mount /scratch --writable-tmpfs"
+}
+
+process {
+    withName: HITE {
+        memory = '64.GB'
+        cpus   = 12
+    }
+}