Merge pull request #40 from Juke34/reditools2

Reditools2

Author: eascarrunz

config/resources/hpc.config

@@ -1,13 +1,6 @@
 process {
     cpus = 1
     time = '1h'
-    maxForks = 12
-    shell = ['/bin/bash', '-euo', 'pipefail']
-    stageOutMode = 'rsync'
-
-    // Enable retries globally for certain exit codes
-    errorStrategy  = { task.attempt <= 3 ? 'retry' : 'finish' }
-
 
     withName: 'fastqc' {
         cpus = 2

nextflow.config

@@ -22,10 +22,16 @@ profiles {
 
     itrop {
         process {
-	   executor = 'slurm'
-	   queue = 'normal'  
-           scratch = '/scratch-ib'
-           clusterOptions = "--constraint=infiniband"
+	   executor        = 'slurm'                // Tells Nextflow to submit jobs using the SLURM workload manager
+           maxForks        = 12                     // Limits the maximum number of jobs that can be submitted concurrently for that process
+           shell           = ['/bin/bash', '-euo', 'pipefail'] // Shell options: -e: Exit immediately on error (non-zero exit status); -u: Treat unset variables as an error; -o pipefail: The pipeline fails if any command in the pipeline fails
+	   queue           = 'normal'               // Submits jobs to the SLURM partition (also called “queue”) named normal.
+	   scratch         = false                  // Use shared file system, not local node /tmp
+	   stageOutMode    = 'move'                 // Move is safe on shared FS and faster than copy
+	   publishDirMode  = 'rsync'                // For final outputs, copy to results folder
+           errorStrategy   = 'retry'                // Retry failing jobs automatically
+	   maxRetries      = 3                      // Retry up to 3 times
+           clusterOptions  = "--constraint=infiniband" // extra parameters provided to the scheduler
         }
 
         singularity.enabled = true

singularity/reditools2/reditools2.def

@@ -26,6 +26,15 @@ From: condaforge/miniforge3:24.7.1-2
     ln -s /opt/reditools2/src/cineca/reditools.py /usr/local/bin/reditools.py
     ln -s /opt/reditools2/src/cineca/parallel_reditools.py /usr/local/bin/parallel_reditools.py
 
+    # Patch hostname retrieval in Reditools2
+    sed -i.bak '849c\
+    addresses = netifaces.ifaddresses(interface)\
+    if netifaces.AF_INET in addresses:\
+        ip_address = addresses[netifaces.AF_INET][0]["addr"]\
+        hostname = socket.gethostbyaddr(ip_address)[0]\
+    else:\
+        hostname = socket.gethostname()' /opt/reditools2/src/cineca/reditools.py
+
 %environment
     export PATH=/usr/local/bin:$PATH
     export CONDA_DEFAULT_ENV=myenv