diff --git a/Snakefile b/Snakefile
index 07999e855..40f25824d 100644
--- a/Snakefile
+++ b/Snakefile
@@ -934,12 +934,16 @@ rule add_lang_tag_corpus_src_for_student:
     threads: workflow.cores
     input: expand(f"{train_student_dir}/corpus.{{lang}}.gz", langpair=langpairs, lang=['source', 'target'])
     output: f"{filtered}/{{langpair}}/corpus.source.langtagged.gz",f"{filtered}/{{langpair}}/corpus.target.gz"
-    params: prefix=f"{filtered}/{{langpair}}/corpus",
+    params: prefix=f"{train_student_dir}/corpus",
             trg_three_letter=lambda wildcards: Language.get(wildcards.langpair.split('-')[1]).to_alpha3(),
-            suffix="source"
-    shell: '''bash pipeline/clean/add-lang-tag.sh "{params.trg_three_letter}" "{params.prefix}" "{o2m_student}" "{params.suffix}" "" >> {log} 2>&1
-            if [ ! -f "{filtered}/{{langpair}}/corpus.target.gz" ]; then cp "{train_student_dir}/{{langpair}}/corpus.target.gz" "{filtered}/{{langpair}}/corpus.target.gz"; fi
-            '''
+            suffix="source",
+            train_dir_langpair=lambda wildcards: f"{train_student_dir}".replace("{langpair}", wildcards.langpair)
+    shell: '''
+        bash pipeline/clean/add-lang-tag.sh "{params.trg_three_letter}" "{params.prefix}" "{o2m_student}" "{params.suffix}" "" >> {log} 2>&1
+        if [ ! -f "{filtered}/{wildcards.langpair}/corpus.target.gz" ]; then
+            cp "{params.train_dir_langpair}/corpus.target.gz" "{filtered}/{wildcards.langpair}/corpus.target.gz";
+        fi
+    '''
 
 rule add_lang_tag_devset_for_student:
     message: "Adding language tag id for devset for student training"
diff --git a/pipeline/clean/add-lang-tag.sh b/pipeline/clean/add-lang-tag.sh
index 84cb793c6..8d9822196 100644
--- a/pipeline/clean/add-lang-tag.sh
+++ b/pipeline/clean/add-lang-tag.sh
@@ -10,6 +10,8 @@ echo "###### Adding language tag"
 
 target_lang_token=$1
 file=$2
+# When we skip Cross-Entropy filtering, we need to move the file from the merged folder to the filtered one.
+outfile="${file/merged/filtered}" 
 o2m=$3
 suffix=$4
 model_dir=$5
@@ -26,13 +28,13 @@ if [ $o2m == "True" ]; then
     target_lang_token=">>${target_lang_token}<< "
     # Check if there is already a language tag token
     if zgrep -q "${target_lang_token}" $file.$lang.gz; then
-        ln -s $file.$lang.gz $file.$suffix.langtagged.gz
+        ln -s $file.$lang.gz $outfile.$suffix.langtagged.gz
         echo "The file already contains language tags, we create a dummy file"
     else
-        zcat $file.$lang.gz | sed "s/^/${target_lang_token}/" | pigz > $file.$suffix.langtagged.gz
+        zcat $file.$lang.gz | sed "s/^/${target_lang_token}/" | pigz > $outfile.$suffix.langtagged.gz
         echo "###### Done: Adding language tag"
     fi
 else
-    ln -s $file.$lang.gz $file.$suffix.langtagged.gz
+    ln -s $file.$lang.gz $outfile.$suffix.langtagged.gz
     echo "The model doesn't have multiple targets, so there is no need to add a language tag, we create a dummy file"
 fi
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