diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml
index 60b33ef21074..b2b79fe33692 100644
--- a/modules/nf-core/trimgalore/environment.yml
+++ b/modules/nf-core/trimgalore/environment.yml
@@ -5,3 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::trim-galore=0.6.10
+  - bioconda::cutadapt=5.2
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
index 0553bb54c4c8..d019d077e43a 100644
--- a/modules/nf-core/trimgalore/main.nf
+++ b/modules/nf-core/trimgalore/main.nf
@@ -46,6 +46,9 @@ process TRIMGALORE {
         def args_list = args.split("\\s(?=--)").toList()
         args_list.removeAll { arg -> arg.toLowerCase().contains('_r2 ') }
         """
+        # Remove any trim_galore outputs left behind by a previous attempt that
+        # ran in this same workdir (e.g. AWS Batch retry after a Spot reclaim).
+        rm -f *.fq.gz *.html *.zip *_trimming_report.txt
         [ ! -f  ${prefix}.fastq.gz ] && ln -s ${reads} ${prefix}.fastq.gz
         trim_galore \\
             ${args_list.join(' ')} \\
@@ -56,6 +59,9 @@ process TRIMGALORE {
     }
     else {
         """
+        # Remove any trim_galore outputs left behind by a previous attempt that
+        # ran in this same workdir (e.g. AWS Batch retry after a Spot reclaim).
+        rm -f *.fq.gz *.html *.zip *_trimming_report.txt
         [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
         [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
         trim_galore \\
diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test
index ac97b087142b..0833eafd25db 100644
--- a/modules/nf-core/trimgalore/tests/main.nf.test
+++ b/modules/nf-core/trimgalore/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
                 { assert snapshot(
                     process.out.reads,
                     file(process.out.log[0][1]).readLines()[0..9], // line 11 changes
-                    file(process.out.log[0][1]).readLines()[11..59],
+                    file(process.out.log[0][1]).readLines()[11..59].findAll { !it.startsWith("This is cutadapt") }, // strip python version
                     process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
@@ -56,9 +56,9 @@ nextflow_process {
                     process.out.reads[0][1][0],
                     process.out.reads[0][1][1],
                     file(process.out.log[0][1][0]).readLines()[0..9], // line 11 changes
-                    file(process.out.log[0][1][0]).readLines()[11..58],
+                    file(process.out.log[0][1][0]).readLines()[11..58].findAll { !it.startsWith("This is cutadapt") }, // strip python version
                     file(process.out.log[0][1][1]).readLines()[0..9], // line 11 changes
-                    file(process.out.log[0][1][1]).readLines()[11..60],
+                    file(process.out.log[0][1][1]).readLines()[11..60].findAll { !it.startsWith("This is cutadapt") }, // strip python version
                     process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
@@ -95,9 +95,9 @@ nextflow_process {
                     process.out.unpaired[0][1][0],
                     process.out.unpaired[0][1][1],
                     file(process.out.log[0][1][0]).readLines()[0..9], // line 11 changes
-                    file(process.out.log[0][1][0]).readLines()[11..59],
+                    file(process.out.log[0][1][0]).readLines()[11..59].findAll { !it.startsWith("This is cutadapt") }, // strip python version
                     file(process.out.log[0][1][1]).readLines()[0..9], // line 11 changes
-                    file(process.out.log[0][1][1]).readLines()[11..63],
+                    file(process.out.log[0][1][1]).readLines()[11..63].findAll { !it.startsWith("This is cutadapt") }, // strip python version
                     process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap
index 2fb55f2d3936..8447b4bc2bdc 100644
--- a/modules/nf-core/trimgalore/tests/main.nf.test.snap
+++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap
@@ -70,7 +70,6 @@
                 "Output file will be GZIP compressed",
                 "",
                 "",
-                "This is cutadapt 5.2 with Python 3.12.12",
                 "Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test_1.fastq.gz",
                 "Processing single-end reads on 1 core ...",
                 "",
@@ -133,7 +132,6 @@
                 "Output file will be GZIP compressed",
                 "",
                 "",
-                "This is cutadapt 5.2 with Python 3.12.12",
                 "Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test_2.fastq.gz",
                 "Processing single-end reads on 1 core ...",
                 "",
@@ -254,7 +252,6 @@
                 "Output file will be GZIP compressed",
                 "",
                 "",
-                "This is cutadapt 5.2 with Python 3.12.12",
                 "Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test_1.fastq.gz",
                 "Processing single-end reads on 1 core ...",
                 "",
@@ -316,7 +313,6 @@
                 "Output file will be GZIP compressed",
                 "",
                 "",
-                "This is cutadapt 5.2 with Python 3.12.12",
                 "Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test_2.fastq.gz",
                 "Processing single-end reads on 1 core ...",
                 "",
@@ -407,7 +403,6 @@
                 "Output file will be GZIP compressed",
                 "",
                 "",
-                "This is cutadapt 5.2 with Python 3.12.12",
                 "Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test.fastq.gz",
                 "Processing single-end reads on 1 core ...",
                 "",