diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1bef9345..4fd7f001 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -39,9 +39,6 @@
     - `samtools/flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
     - `samtools/idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
 
-* `umi_tools`:
-    - `umi_tools/umi_tools_dedup`: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read (PR #).
-    
 ## MAJOR CHANGES
 
 ## MINOR CHANGES
diff --git a/src/umi_tools/umi_tools_dedup/config.vsh.yaml b/src/umi_tools/umi_tools_dedup/config.vsh.yaml
deleted file mode 100644
index 75306541..00000000
--- a/src/umi_tools/umi_tools_dedup/config.vsh.yaml
+++ /dev/null
@@ -1,279 +0,0 @@
-name: umi_tool_dedup
-namespace: umi_tools
-description: |
-  Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
-keywords: [umi_tools, deduplication, dedup]
-links:
-  homepage: https://umi-tools.readthedocs.io/en/latest/
-  documentation: [ https://umi-tools.readthedocs.io/en/latest/reference/dedup.html,
-                   https://umi-tools.readthedocs.io/en/latest/common_options.html#common-options ]
-  repository: https://github.com/CGATOxford/UMI-tools
-references: 
-  doi: 10.1101/gr.209601.116
-license: MIT
-
-argument_groups:
-  - name: Inputs
-    arguments:
-      - name: --input
-        alternatives: -I
-        type: file
-        description: Input BAM or SAM file. Use --in_sam to specify SAM format.
-        required: true
-      - name: --in_sam
-        type: boolean_true
-        description: |
-          By default, inputs are assumed to be in BAM format. Use this options 
-          to specify the use of SAM format for input.
-      - name: --bai
-        type: file
-        description: BAM index
-      - name: --get_output_stats
-        type: boolean
-        description: Whether or not to generate output stats. 
-      - name: --random_seed
-        type: integer
-        description: |
-          Random seed to initialize number generator with.
-        default: none
-
-  - name: Outputs
-    arguments:
-      - name: --output
-        alternatives: -S
-        type: file
-        description: Deduplicated BAM file
-        required: true
-        direction: output
-      - name: --out_sam
-        type: boolean_true
-        description: |
-          By default, outputa are written in BAM format. Use this options to 
-          specify the use of SAM format for output.
-      - name: --paired
-        type: boolean_true
-        description: |
-          BAM is paired end - output both read pairs. This will also force the
-          use of the template length to determine reads with the same mapping
-          coordinates.
-      - name: --output_stats
-        type: file
-        description: Directory containing UMI based deduplication statistics files
-        direction: output
-      - name: --extract_umi_method
-        type: string
-        description: |
-          Specify the method by which the barcodes were encoded in the read.
-          The options are: [read_id, tag, umis].
-        default: read_id
-      - name: --umi_tag
-        type: string
-        description: |
-          The tag containing the UMI sequence. 
-          This is only required if the extract_umi_method is set to tag.
-      - name: --umi_separator
-        type: string
-        description: |
-          The separator used to separate the UMI from the read sequence. 
-          This is only required if the extract_umi_method is set to id_read.
-        default: '_'
-      - name: --umi_tag_split
-        type: string
-        description: |
-          Separate the UMI in tag by <SPLIT> and take the first element.
-      - name: --umi_tag_delimiter
-        type: string
-        description: |
-          Separate the UMI in by <DELIMITER> and concatenate the elements
-      - name: --cell_tag
-        type: string
-        description: |
-          The tag containing the cell barcode sequence. 
-          This is only required if the extract_umi_method is set to tag.
-      - name: --cell_tag_split
-        type: string
-        description: |
-          Separate the cell barcode in tag by <SPLIT> and take the first element.
-      - name: --cell_tag_delimiter
-        type: string
-        description: |
-          Separate the cell barcode in by <DELIMITER> and concatenate the elements
-  
-  - name: Grouping Options
-    arguments:    
-      - name: --method
-        type: string
-        description: |
-          The method to use for grouping reads. The options are: 
-          [unique, percentile, cluster, adjacency, directional].
-        default: directional
-      - name: --edit_distance_threshold
-        type: integer
-        description: |
-          For the adjacency and cluster methods the threshold for the edit 
-          distance to connect two UMIs in the network can be increased. The 
-          default value of 1 works best unless the UMI is very long (>14bp).
-        default: 1
-      - name: --spliced_is_unique
-        type: boolean_true
-        description: |
-          Causes two reads that start in the same position on the same strand
-          and having the same UMI to be considered unique if one is spliced 
-          and the other is not. (Uses the ‘N’ cigar operation to test for splicing).
-      - name: --soft_clip_threshold
-        type: integer
-        description: |
-          Mappers that soft clip will sometimes do so rather than mapping a
-          spliced read if there is only a small overhang over the exon junction.
-          By setting this option, you can treat reads with at least this many
-          bases soft-clipped at the 3’ end as spliced.
-        default: 4
-      - name: --multimapping_detection_method
-        type: string
-        description: |
-          If the sam/bam contains tags to identify multimapping reads, you can
-          specify for use when selecting the best read at a given loci. Supported
-          tags are “NH”, “X0” and “XT”. If not specified, the read with the highest
-          mapping quality will be selected.
-      - name: --read_length
-        type: integer
-        description: |
-          Use the read length as a criteria when deduping, for e.g sRNA-Seq.
-  
-  - name: Single-cell RNA-Seq Options
-    arguments:
-      - name: --per_gene
-        type: boolean_true
-        description: |
-          Reads will be grouped together if they have the same gene. This is useful
-          if your library prep generates PCR duplicates with non identical alignment
-          positions such as CEL-Seq. Note this option is hardcoded to be on with the
-          count command. I.e counting is always performed per-gene. Must be combined
-          with either --gene_tag or --per_contig option.
-      - name: --gene_tag
-        type: string
-        description: |
-          Deduplicate per gene. The gene information is encoded in the bam read tag
-          specified.
-      - name: --assigned_status_tag
-        type: string
-        description: |
-          BAM tag which describes whether a read is assigned to a gene. Defaults to
-          the same value as given for --gene_tag.
-      - name: --skip_tags_regex
-        type: string
-        description: |
-          Use in conjunction with the --assigned_status_tag option to skip any reads
-          where the tag matches this regex. Default ("^[__|Unassigned]") matches
-          anything which starts with “__” or “Unassigned”.
-      - name: --per_contig
-        type: boolean_true
-        description: |
-          Deduplicate per contig (field 3 in BAM; RNAME). All reads with the same
-          contig will be considered to have the same alignment position. This is
-          useful if you have aligned to a reference transcriptome with one
-          transcript per gene. If you have aligned to a transcriptome with more
-          than one transcript per gene, you can supply a map between transcripts
-          and gene using the --gene_transcript_map option.
-      - name: --gene_transcript_map
-        type: file
-        description: |
-          A file containing a mapping between gene names and transcript names.
-          The file should be tab separated with the gene name in the first column
-          and the transcript name in the second column.
-      - name: --per_cell
-        type: boolean_true
-        description: |
-          Reads will only be grouped together if they have the same cell barcode.
-          Can be combined with --per_gene.
-  
-  - name: SAM/BAM Options
-    arguments:
-      - name: --mapping_quality
-        type: integer
-        description: |
-          Minimium mapping quality (MAPQ) for a read to be retained.
-        default: 0
-      - name: --unmapped_reads
-        type: string
-        description: |
-          How unmapped reads should be handled. 
-          The options are:
-          "discard": Discard all unmapped reads.
-          "use":     If read2 is unmapped, deduplicate using read1 only. 
-                     Requires --paired.
-          "output":  Output unmapped reads/read pairs without UMI 
-                     grouping/deduplication. Only available in umi_tools group.
-        default: discard
-      - name: --chimeric_pairs
-        type: string
-        description: |
-          How chimeric pairs should be handled. 
-          The options are:
-          "discard": Discard all chimeric read pairs.
-          "use":     Deduplicate using read1 only.
-          "output":  Output chimeric pairs without UMI grouping/deduplication. 
-                     Only available in umi_tools group.
-        default: use
-      - name: --unapired_reads
-        type: string
-        description: |
-          How unpaired reads should be handled. 
-          The options are:
-          "discard": Discard all unpaired reads.
-          "use":     Deduplicate using read1 only.
-          "output":  Output unpaired reads without UMI grouping/deduplication. 
-                     Only available in umi_tools group.
-        default: use
-      - name: --ignore_umi
-        type: boolean_true
-        description: |
-          Ignore the UMI and group reads using mapping coordinates only.
-      - name: --subset
-        type: boolean_true
-        description: |
-          Only consider a fraction of the reads, chosen at random. This is useful
-          for doing saturation analyses.
-      - name: --chrom
-        type: string
-        description: |
-          Only consider a single chromosome. This is useful for debugging/testing 
-          purposes.
-  
-  - name: Group/Dedup Options
-    arguments:
-      - name: --no_sort_output
-        type: boolean_true
-        description: |
-          By default, output is sorted. This involves the use of a temporary unsorted
-          file (saved in --temp-dir). Use this option to turn off sorting.
-      - name: --buffer_whole_contig
-        type: boolean_true
-        description: |
-          Forces dedup to parse an entire contig before yielding any reads for
-          deduplication. This is the only way to absolutely guarantee that all reads
-          with the same start position are grouped together for deduplication since
-          dedup uses the start position of the read, not the alignment coordinate on
-          which the reads are sorted. However, by default, dedup reads for another
-          1000bp before outputting read groups which will avoid any reads being missed
-          with short read sequencing (<1000bp).
-
-
-resources:
-  - type: bash_script
-    path: script.sh
-test_resources:
-  - type: bash_script
-    path: test.sh
-  - type: file
-    path: test_data
-engines:
-  - type: docker
-    image: quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1
-    setup:
-      - type: docker
-        run: |
-            umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
-runners:
-- type: executable
-- type: nextflow
\ No newline at end of file
diff --git a/src/umi_tools/umi_tools_dedup/help.txt b/src/umi_tools/umi_tools_dedup/help.txt
deleted file mode 100644
index d3c8fa44..00000000
--- a/src/umi_tools/umi_tools_dedup/help.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-```
-umi_tools dedup
-```
-
-dedup - Deduplicate reads using UMI and mapping coordinates
-
-Usage: umi_tools dedup [OPTIONS] [--stdin=IN_BAM] [--stdout=OUT_BAM]
-
-       note: If --stdout is ommited, standard out is output. To
-             generate a valid BAM file on standard out, please
-             redirect log with --log=LOGFILE or --log2stderr 
-
-For full UMI-tools documentation, see https://umi-tools.readthedocs.io/en/latest/
\ No newline at end of file
diff --git a/src/umi_tools/umi_tools_dedup/script.sh b/src/umi_tools/umi_tools_dedup/script.sh
deleted file mode 100644
index 57c01258..00000000
--- a/src/umi_tools/umi_tools_dedup/script.sh
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/bin/bash
-
-## VIASH START
-## VIASH END
-
-set -e
-
-test_dir="${metal_executable}/test_data"
-
-[[ "$par_paired" == "false" ]] && unset par_paired
-[[ "$par_in_sam" == "false" ]] && unset par_in_sam
-[[ "$par_out_sam" == "false" ]] && unset par_out_sam
-[[ "$par_spliced_is_unique" == "false" ]] && unset par_spliced_is_unique
-[[ "$par_per_gene" == "false" ]] && unset par_per_gene
-[[ "$par_per_contig" == "false" ]] && unset par_per_contig
-[[ "$par_per_cell" == "false" ]] && unset par_per_cell
-[[ "$par_no_sort_output" == "false" ]] && unset par_no_sort_output
-[[ "$par_buffer_whole_contig" == "false" ]] && unset par_buffer_whole_contig
-[[ "$par_ignore_umi" == "false" ]] && unset par_ignore_umi
-[[ "$par_subset" == "false" ]] && unset par_subset
-
-
-$(which umi_tools) dedup \
-    -I "$par_input" \
-    ${par_in_sam:+--in-sam} \
-    ${par_bai:+--bai "$par_bai"} \
-    ${par_get_output_stats:+--get-output-stats} \
-    ${par_random_seed:+--random-seed "$par_random_seed"} \
-    -S "$par_output" \
-    ${par_out_sam:+--out-sam} \
-    ${par_paired:+--paired} \
-    ${par_output_stats:+--output-stats "$par_output_stats"} \
-    ${par_extract_umi_method:+--extract-umi-method "$par_extract_umi_method"} \
-    ${par_umi_tag:+--umi-tag "$par_umi_tag"} \
-    ${par_umi_separator:+--umi-separator "$par_umi_separator"} \
-    ${par_umi_tag_split:+--umi-tag-split "$par_umi_tag_split"} \
-    ${par_umi_tag_delimiter:+--umi-tag-delimiter "$par_umi_tag_delimiter"} \
-    ${par_cell_tag:+--cell-tag "$par_cell_tag"} \
-    ${par_cell_tag_split:+--cell-tag-split "$par_cell_tag_split"} \
-    ${par_cell_tag_delimiter:+--cell-tag-delimiter "$par_cell_tag_delimiter"} \
-    ${par_method:+--method "$par_method"} \
-    ${par_edit_distance_threshold:+--edit-distance-threshold "$par_edit_distance_threshold"} \
-    ${par_spliced_is_unique:+--spliced-is-unique} \
-    ${par_soft_clip_threshold:+--soft-clip-threshold "$par_soft_clip_threshold"} \
-    ${par_multimapping_detection_method:+--multimapping-detection-method "$par_multimapping_detection_method"} \
-    ${par_read_length:+--read-length "$par_read_length"} \
-    ${par_per_gene:+--per-gene} \
-    ${par_gene_tag:+--gene-tag "$par_gene_tag"} \
-    ${par_assigned_status_tag:+--assigned-status-tag "$par_assigned_status_tag"} \
-    ${par_skip_tags_regex:+--skip-tags-regex "$par_skip_tags_regex"} \
-    ${par_per_contig:+--per-contig}
-    ${par_gene_transcript_map:+--gene-transcript-map "$par_gene_transcript_map"} \
-    ${par_per_cell:+--per-cell} \
-    ${par_mapping_quality:+--mapping-quality "$par_mapping_quality"} \
-    ${par_unmapped_reads:+--unmapped-reads "$par_unmapped_reads"} \
-    ${par_chimeric_pairs:+--chimeric-pairs "$par_chimeric_pairs"} \
-    ${par_unapired_reads:+--unapired-reads "$par_unapired_reads"} \
-    ${par_ignore_umi:+--ignore-umi} \
-    ${par_subset:+--subset} \
-    ${par_chrom:+--chrom "$par_chrom"} \
-    ${par_no_sort_output:+--no-sort-output} \
-    ${par_buffer_whole_contig:+--buffer-whole-contig}
-
-
-exit 0
\ No newline at end of file
diff --git a/src/umi_tools/umi_tools_dedup/test.sh b/src/umi_tools/umi_tools_dedup/test.sh
deleted file mode 100644
index 1459ec08..00000000
--- a/src/umi_tools/umi_tools_dedup/test.sh
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/bin/bash
-
-test_dir="${meta_resources_dir}/test_data"
-echo ">>> Testing $meta_functionality_name"
-
-"$meta_executable" \
-  --bam "$test_dir/a.sorted.bam" \
-  --bai "$test_dir/a.sorted.bam.bai" \
-  --output "$test_dir/a.sorted.idxstats"
-
-echo ">>> Checking whether output exists"
-[ ! -f "$test_dir/a.sorted.idxstats" ] && echo "File 'a.sorted.idxstats' does not exist!" && exit 1
-
-echo ">>> Checking whether output is non-empty"
-[ ! -s "$test_dir/a.sorted.idxstats" ] && echo "File 'a.sorted.idxstats' is empty!" && exit 1
-
-echo ">>> Checking whether output is correct"
-diff "$test_dir/a.sorted.idxstats" "$test_dir/a_ref.sorted.idxstats" || \
-    (echo "Output file a.sorted.idxstats does not match expected output" && exit 1)
-
-rm "$test_dir/a.sorted.idxstats"
-
-############################################################################################
-
-echo ">>> Testing $meta_functionality_name with singletons in the input"
-
-"$meta_executable" \
-  --bam "$test_dir/test.paired_end.sorted.bam" \
-  --bai "$test_dir/test.paired_end.sorted.bam.bai" \
-  --output "$test_dir/test.paired_end.sorted.idxstats"
-
-echo ">>> Checking whether output exists"
-[ ! -f "$test_dir/test.paired_end.sorted.idxstats" ] && \
-    echo "File 'test.paired_end.sorted.idxstats' does not exist!" && exit 1
-
-echo ">>> Checking whether output is non-empty"
-[ ! -s "$test_dir/test.paired_end.sorted.idxstats" ] && \
-    echo "File 'test.paired_end.sorted.idxstats' is empty!" && exit 1
-
-echo ">>> Checking whether output is correct"
-diff "$test_dir/test.paired_end.sorted.idxstats" "$test_dir/test_ref.paired_end.sorted.idxstats" || \
-    (echo "Output file test.paired_end.sorted.idxstats does not match expected output" && exit 1)
-
-rm "$test_dir/test.paired_end.sorted.idxstats"
-
-############################################################################################
-
-echo "All tests succeeded!"
-exit 0
\ No newline at end of file