diff --git a/modules.json b/modules.json
index fe8f75cc..c0c4132a 100644
--- a/modules.json
+++ b/modules.json
@@ -42,7 +42,7 @@
                     },
                     "custom/shortenfastaids": {
                         "branch": "main",
-                        "git_sha": "e226301053a2b0f9a6af514b454b3ae7c91daa80",
+                        "git_sha": "e9ec2e4c48ead3d760c8e13950c568c19ae86b8b",
                         "installed_by": ["fasta_ltrretriever_lai"]
                     },
                     "gffread": {
@@ -121,7 +121,7 @@
                     },
                     "fasta_ltrretriever_lai": {
                         "branch": "main",
-                        "git_sha": "734297c99ae8b13ed73e3ff9a8f1215e1ca05ecd",
+                        "git_sha": "e9ec2e4c48ead3d760c8e13950c568c19ae86b8b",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_bwa_mem_samblaster": {
diff --git a/modules/pfr/custom/shortenfastaids/main.nf b/modules/pfr/custom/shortenfastaids/main.nf
index cef0796c..3cdaa07c 100644
--- a/modules/pfr/custom/shortenfastaids/main.nf
+++ b/modules/pfr/custom/shortenfastaids/main.nf
@@ -25,7 +25,10 @@ process CUSTOM_SHORTENFASTAIDS {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch "${meta.id}.short.ids.tsv"
+    echo \\
+        'IDs have acceptable length and character. No change required.' \\
+        > ${meta.id}.short.ids.tsv
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version | cut -d' ' -f2)
diff --git a/modules/pfr/custom/shortenfastaids/tests/main.nf.test.snap b/modules/pfr/custom/shortenfastaids/tests/main.nf.test.snap
index 49fa2afb..2506ebd6 100644
--- a/modules/pfr/custom/shortenfastaids/tests/main.nf.test.snap
+++ b/modules/pfr/custom/shortenfastaids/tests/main.nf.test.snap
@@ -59,7 +59,7 @@
                         {
                             "id": "test"
                         },
-                        "test.short.ids.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.short.ids.tsv:md5,fcf920d9a7b57a1e3c29a9e88673330f"
                     ]
                 ],
                 "2": [
@@ -73,7 +73,7 @@
                         {
                             "id": "test"
                         },
-                        "test.short.ids.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.short.ids.tsv:md5,fcf920d9a7b57a1e3c29a9e88673330f"
                     ]
                 ],
                 "versions": [
@@ -83,9 +83,9 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-02T20:54:36.815875"
+        "timestamp": "2024-06-04T13:58:30.161542"
     },
     "homo_sapiens-genome_fasta-no_change": {
         "content": [
diff --git a/subworkflows/pfr/fasta_ltrretriever_lai/main.nf b/subworkflows/pfr/fasta_ltrretriever_lai/main.nf
index b63f8ea1..3820e69c 100644
--- a/subworkflows/pfr/fasta_ltrretriever_lai/main.nf
+++ b/subworkflows/pfr/fasta_ltrretriever_lai/main.nf
@@ -174,23 +174,23 @@ workflow FASTA_LTRRETRIEVER_LAI {
 
 def map_monoploid_seqs_to_new_ids(id, short_ids_tsv, monoploid_seqs) {
 
-    def short_ids_head = short_ids_tsv.text.split('\n')[0]
+    def short_ids_head = short_ids_tsv.text.tokenize('\n')[0]
 
     if (short_ids_head == "IDs have acceptable length and character. No change required.") {
-        return [ "${id}.mapped.monoploid.seqs.txt" ] + monoploid_seqs.text.split('\n')
+        return [ "${id}.mapped.monoploid.seqs.txt" ] + monoploid_seqs.text.tokenize('\n')
     }
 
     def orig_to_new_ids = [:]
     short_ids_tsv.text.eachLine { line ->
-        def (original_id, renamed_id) = line.split('\t')
+        def (original_id, renamed_id) = line.tokenize('\t')
         orig_to_new_ids[original_id] = renamed_id
     }
 
     def mapped_ids = []
     monoploid_seqs.text.eachLine { original_id ->
         if (!orig_to_new_ids[original_id]) {
-            error "Faild to find $original_id in ${monoploid_seqs}" +
-            "The monoploid_seqs file is malformed!"
+            error "Faild to find $original_id in ${short_ids_tsv}" +
+            "\nThe short_ids_tsv file is malformed!"
         }
 
         mapped_ids.add(orig_to_new_ids[original_id])
diff --git a/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test b/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test
index 192ccef6..a7fc65eb 100644
--- a/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test
+++ b/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test
@@ -135,9 +135,9 @@ nextflow_workflow {
             workflow {
                 """
                 def monoploid_seqs  = new File('test.mono.seq.txt')
-                monoploid_seqs.write("chr_xxxxxxxxxxxxxxx_1")
+                monoploid_seqs.write("chr1")
 
-                input[0]            = Channel.empty()
+                input[0]            = GUNZIP.out.gunzip
                 input[1]            = Channel.of( [ [ id:'test' ], monoploid_seqs.toPath() ] )
                 input[2]            = false
                 """
diff --git a/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test.snap b/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test.snap
index 4ce42ec1..e827219f 100644
--- a/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test.snap
+++ b/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test.snap
@@ -56,41 +56,91 @@
         "content": [
             {
                 "0": [
-
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.LTRlib.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "1": [
-
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.out.gff3:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "2": [
-
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.LAI.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "3": [
-
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.LAI.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "4": [
-
+                    "versions.yml:md5,05a74dacbcd6c5906faeca3206f6563f",
+                    "versions.yml:md5,52a98b45c3cf73f9314dbe9b34eca9d8",
+                    "versions.yml:md5,5d86cda262f5c21e43738433a2781ebc",
+                    "versions.yml:md5,608d746d45680f025562c4be455db461",
+                    "versions.yml:md5,8468404805dddec679524e75b4fa51e8",
+                    "versions.yml:md5,fb42c6cc5c28b6f9d3384171c7b6b143"
                 ],
                 "annotation_gff": [
-
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.out.gff3:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "lai_log": [
-
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.LAI.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "lai_out": [
-
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.LAI.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "ltrlib": [
-
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.LTRlib.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "versions": [
-
+                    "versions.yml:md5,05a74dacbcd6c5906faeca3206f6563f",
+                    "versions.yml:md5,52a98b45c3cf73f9314dbe9b34eca9d8",
+                    "versions.yml:md5,5d86cda262f5c21e43738433a2781ebc",
+                    "versions.yml:md5,608d746d45680f025562c4be455db461",
+                    "versions.yml:md5,8468404805dddec679524e75b4fa51e8",
+                    "versions.yml:md5,fb42c6cc5c28b6f9d3384171c7b6b143"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-02T20:35:25.114358"
+        "timestamp": "2024-06-04T13:50:48.75158"
     }
-}
+}
\ No newline at end of file