diff --git a/CHANGELOG.md b/CHANGELOG.md
index cff45bfa..e77efb23 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 🔙 Reverted PR #523 which changes subworkflows directly in the pipeline.
 - 🔄 Updated template to nf-core/tools v3.2.0 [#](https://github.com/nf-core/methylseq/pull/)
 - 🐛 bumped the minimum for `PARABRICKS_FQ2BAMMETH` to 100.GB as suggested by the docs [#528](https://github.com/nf-core/methylseq/issues/528)
+- 🐛 fix parabricks/fq2bammeth failure on AWS Batch like executors where symlinks don't exist [#536](https://github.com/nf-core/methylseq/issues/536)
 
 ### Pipeline Updates
 
diff --git a/modules.json b/modules.json
index dad1add5..845596f4 100644
--- a/modules.json
+++ b/modules.json
@@ -82,7 +82,7 @@
                     },
                     "parabricks/fq2bammeth": {
                         "branch": "master",
-                        "git_sha": "2edb63067971fb906749e96bf22b23a4ec892a62",
+                        "git_sha": "ca2409607b2095e8ad375c990f256b418caedd0f",
                         "installed_by": ["fastq_align_dedup_bwameth"]
                     },
                     "picard/markduplicates": {
diff --git a/modules/nf-core/parabricks/fq2bammeth/main.nf b/modules/nf-core/parabricks/fq2bammeth/main.nf
index eb7ae685..456413af 100644
--- a/modules/nf-core/parabricks/fq2bammeth/main.nf
+++ b/modules/nf-core/parabricks/fq2bammeth/main.nf
@@ -34,7 +34,11 @@ process PARABRICKS_FQ2BAMMETH {
     def known_sites_output  = known_sites ? "--out-recal-file ${prefix}.table" : ""
     def num_gpus            = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
-    ln -sf \$(readlink $fasta) $index/$fasta
+    if [ -L $fasta ]; then
+        ln -sf \$(readlink $fasta) $index/$fasta
+    else
+        ln -sf ../$fasta $index/$fasta
+    fi
 
     pbrun \\
         fq2bam_meth \\
diff --git a/modules/nf-core/parabricks/fq2bammeth/meta.yml b/modules/nf-core/parabricks/fq2bammeth/meta.yml
index 4f295b88..5128f577 100644
--- a/modules/nf-core/parabricks/fq2bammeth/meta.yml
+++ b/modules/nf-core/parabricks/fq2bammeth/meta.yml
@@ -10,7 +10,7 @@ tools:
   - "parabricks":
       description: "NVIDIA Clara Parabricks GPU-accelerated genomics tools"
       homepage: "https://www.nvidia.com/en-us/clara/genomics/"
-      documentation: "https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html#fq2bam-meth-reference"
+      documentation: "https://docs.nvidia.com/clara/parabricks/latest/index.html"
       licence: ["custom"]
       identifier: ""
 
@@ -80,7 +80,7 @@ output:
   - duplicate_metrics:
       - duplicate-metrics.txt:
           type: file
-          description: (optional) metrics calculated from marking duplcates in the bam
+          description: (optional) metrics calculated from marking duplicates in the bam
             file
           pattern: "*-duplicate-metrics.txt"
   - versions:
diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
index ce89e8ca..7123c566 100644
--- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
+++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [ id:'test' ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
                 ])
                 """
             }
@@ -34,12 +34,12 @@ nextflow_process {
                 input[0] = Channel.of([
 				    [ id:'test', single_end:true ], // meta map
 				    [
-				        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/illumina/SRR389222_sub1.fastq.gz', checkIfExists: true)
 				    ]
 				])
                 input[1] = Channel.of([
                     [ id:'test' ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
                 ])
 				input[2] = BWAMETH_INDEX.out.index
                 input[3] = []
@@ -68,12 +68,12 @@ nextflow_process {
                 input[0] = Channel.of([
 				    [ id:'test', single_end:true ], // meta map
 				    [
-				        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/illumina/SRR389222_sub1.fastq.gz', checkIfExists: true)
 				    ]
 				])
                 input[1] = Channel.of([
                     [ id:'test' ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
                 ])
 				input[2] = BWAMETH_INDEX.out.index
                 input[3] = []
@@ -98,13 +98,13 @@ nextflow_process {
                 input[0] = Channel.of([
 				    [ id:'test', single_end:false ], // meta map
 				    [
-				        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true),
-                        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/illumina/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/illumina/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true),
 				    ]
 				])
                 input[1] = Channel.of([
                     [ id:'test' ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
                 ])
 				input[2] = BWAMETH_INDEX.out.index
                 input[3] = []