From 4cac1278b9c4a96aebcc8185d8df834fee9a7a87 Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Thu, 11 Apr 2024 11:50:45 +0100
Subject: [PATCH] Initial commit for umi-tools dedup

---
 src/umi_tools/umi_tools_dedup/config.vsh.yaml | 279 ++++++++++++++++++
 src/umi_tools/umi_tools_dedup/help.txt        |  13 +
 src/umi_tools/umi_tools_dedup/script.sh       |  65 ++++
 src/umi_tools/umi_tools_dedup/test.sh         |  49 +++
 4 files changed, 406 insertions(+)
 create mode 100644 src/umi_tools/umi_tools_dedup/config.vsh.yaml
 create mode 100644 src/umi_tools/umi_tools_dedup/help.txt
 create mode 100644 src/umi_tools/umi_tools_dedup/script.sh
 create mode 100644 src/umi_tools/umi_tools_dedup/test.sh

diff --git a/src/umi_tools/umi_tools_dedup/config.vsh.yaml b/src/umi_tools/umi_tools_dedup/config.vsh.yaml
new file mode 100644
index 00000000..75306541
--- /dev/null
+++ b/src/umi_tools/umi_tools_dedup/config.vsh.yaml
@@ -0,0 +1,279 @@
+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
new file mode 100644
index 00000000..d3c8fa44
--- /dev/null
+++ b/src/umi_tools/umi_tools_dedup/help.txt
@@ -0,0 +1,13 @@
+```
+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
new file mode 100644
index 00000000..57c01258
--- /dev/null
+++ b/src/umi_tools/umi_tools_dedup/script.sh
@@ -0,0 +1,65 @@
+#!/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} \
+    ${par_buffer_whole_contig:+--buffer-whole-contig}
+
+
+exit 0
\ No newline at end of file
diff --git a/src/umi_tools/umi_tools_dedup/test.sh b/src/umi_tools/umi_tools_dedup/test.sh
new file mode 100644
index 00000000..1459ec08
--- /dev/null
+++ b/src/umi_tools/umi_tools_dedup/test.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+test_dir="${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