From 38adb65018141180b9ede9ddedece9e40ac6be57 Mon Sep 17 00:00:00 2001
From: ens-ftricomi <ftricomi@ebi.ac.uk>
Date: Wed, 14 Aug 2024 14:31:51 +0100
Subject: [PATCH] retry when file reading didn't work

---
 .../transcriptomic_alignment/index_genome.nf  | 20 +++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
index af203c2..c3ab961 100644
--- a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
+++ b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
@@ -47,11 +47,15 @@ process INDEX_GENOME {
     // Initialize variables
     def numberOfReferences = 0
     def genomeLength = 0
-    // Read the FASTA file line by line
-    genomefilePath.eachLine { line ->
-        if (line.startsWith('>')) {
-            numberOfReferences++
-        } else {
+    def retryCount = 0
+    def maxRetries = 3
+    def filesValid = false
+    while (!filesValid && retryCount < maxRetries) {
+        // Read the FASTA file line by line
+        genomefilePath.eachLine { line ->
+            if (line.startsWith('>')) {
+                numberOfReferences++
+            } else {
             genomeLength += line.trim().length()
         }
     }
@@ -66,6 +70,10 @@ process INDEX_GENOME {
     // Calculate the genome length (excluding header lines)
     //def genomeLength = fastaContent.split('\n').findAll { !it.startsWith('>') }.join('').length()
 
+     if (genomeLength != 0) {
+       filesValid = true
+        }
+    }
     // Define read length (you may need to adjust this based on your data)
     def readLength = 100
 
@@ -97,6 +105,6 @@ process INDEX_GENOME {
     """
     }
 
-    }
+}