diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t10_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t10_1_trimmomatic.err
new file mode 100755
index 00000000..0e40b55a
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t10_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807201
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 68758964 Both Surviving: 68738356 (99.97%) Forward Only Surviving: 4329 (0.01%) Reverse Only Surviving: 6139 (0.01%) Dropped: 10140 (0.01%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t11_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t11_1_trimmomatic.err
new file mode 100755
index 00000000..6431353e
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t11_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23820432
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 36757610 Both Surviving: 36747933 (99.97%) Forward Only Surviving: 2407 (0.01%) Reverse Only Surviving: 3687 (0.01%) Dropped: 3583 (0.01%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t12_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t12_1_trimmomatic.err
new file mode 100755
index 00000000..4e061392
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t12_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807210
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 22377822 Both Surviving: 22368123 (99.96%) Forward Only Surviving: 4068 (0.02%) Reverse Only Surviving: 5630 (0.03%) Dropped: 1 (0.00%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t1_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t1_1_trimmomatic.err
new file mode 100755
index 00000000..2882a0c5
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t1_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807202
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 22377822 Both Surviving: 22368011 (99.96%) Forward Only Surviving: 4745 (0.02%) Reverse Only Surviving: 5065 (0.02%) Dropped: 1 (0.00%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t3_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t3_1_trimmomatic.err
new file mode 100755
index 00000000..b2eaa9f3
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t3_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807206
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 68777345 Both Surviving: 68767299 (99.99%) Forward Only Surviving: 1952 (0.00%) Reverse Only Surviving: 3622 (0.01%) Dropped: 4472 (0.01%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t4_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t4_1_trimmomatic.err
new file mode 100755
index 00000000..14ba2215
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t4_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807214
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 58558991 Both Surviving: 58544996 (99.98%) Forward Only Surviving: 3031 (0.01%) Reverse Only Surviving: 4723 (0.01%) Dropped: 6241 (0.01%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t5_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t5_1_trimmomatic.err
new file mode 100755
index 00000000..2feea475
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t5_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807212
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 91645932 Both Surviving: 91623858 (99.98%) Forward Only Surviving: 3779 (0.00%) Reverse Only Surviving: 6136 (0.01%) Dropped: 12159 (0.01%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t6_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t6_1_trimmomatic.err
new file mode 100755
index 00000000..7b253fe7
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t6_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807219
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 58633103 Both Surviving: 58625158 (99.99%) Forward Only Surviving: 1983 (0.00%) Reverse Only Surviving: 3642 (0.01%) Dropped: 2320 (0.00%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t8_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t8_1_trimmomatic.err
new file mode 100755
index 00000000..0ec84348
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t8_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807217
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 16990806 Both Surviving: 16986783 (99.98%) Forward Only Surviving: 847 (0.00%) Reverse Only Surviving: 1584 (0.01%) Dropped: 1592 (0.01%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/180518_mATAC_t9_1_trimmomatic.err b/data/modules/trimmomatic/issue_864/180518_mATAC_t9_1_trimmomatic.err
new file mode 100755
index 00000000..f8bbf2b3
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/180518_mATAC_t9_1_trimmomatic.err
@@ -0,0 +1,12 @@
+Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807221
+TrimmomaticPE: Started with arguments:
+ -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog
+Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
+Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
+ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Quality encoding detected as phred33
+Input Read Pairs: 56406356 Both Surviving: 56379957 (99.95%) Forward Only Surviving: 3801 (0.01%) Reverse Only Surviving: 15581 (0.03%) Dropped: 7017 (0.01%)
+TrimmomaticPE: Completed successfully
diff --git a/data/modules/trimmomatic/issue_864/multiqc_config.yaml b/data/modules/trimmomatic/issue_864/multiqc_config.yaml
new file mode 100755
index 00000000..df2fd13f
--- /dev/null
+++ b/data/modules/trimmomatic/issue_864/multiqc_config.yaml
@@ -0,0 +1,2 @@
+trimmomatic:
+    s_name_filenames: true