Merge branch 'main' into samtools_sort

CHANGELOG.md

@@ -36,10 +36,11 @@
     - `salmon/salmon_quant`: Transcript quantification from RNA-seq data (PR #24).
 
 * `samtools`:
-    - `samtools/samtools_flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
-    - `samtools/samtools_idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
+    - `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).
     - `samtools/samtools_index`: Index SAM/BAM/CRAM files (PR #35).
     - `samtools/samtools_sort`: Sort SAM/BAM/CRAM files (PR #36).
+    - `samtools/samtools_stats`: Reports alignment summary statistics for a BAM file (PR #39).
 
 ## MAJOR CHANGES
 

src/samtools/samtools_stats/config.vsh.yaml

@@ -0,0 +1,166 @@
+name: samtools_stats
+namespace: samtools
+description: Reports alignment summary statistics for a BAM file.
+keywords: [statistics, counts, bam, sam, cram]
+links:
+  homepage: https://www.htslib.org/
+  documentation: https://www.htslib.org/doc/samtools-idxstats.html
+  repository: https://github.com/samtools/samtools
+references: 
+  doi: 10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008
+license: MIT/Expat
+
+argument_groups:
+  - name: Inputs
+    arguments:
+    - name: --input
+      type: file
+      description: |
+        Input file.
+      required: true
+      must_exist: true
+    - name: --bai
+      type: file
+      description: |
+        Index file.
+    - name: --fasta
+      type: file
+      description: |
+        Reference file the CRAM was created with.
+    - name: --coverage
+      alternatives: -c
+      type: integer
+      description: |
+        Coverage distribution min,max,step [1,1000,1].
+      multiple: true
+      multiple_sep: ','
+    - name: --remove_dups
+      alternatives: -d
+      type: boolean_true
+      description: |
+        Exclude from statistics reads marked as duplicates.
+    - name: --customized_index_file
+      alternatives: -X 
+      type: boolean_true
+      description: |
+        Use a customized index file.
+    - name: --required_flag
+      alternatives: -f
+      type: string
+      description: |
+        Required flag, 0 for unset. See also `samtools flags`.
+      default: "0"
+    - name: --filtering_flag
+      alternatives: -F
+      type: string
+      description: |
+        Filtering flag, 0 for unset. See also `samtools flags`.
+      default: "0"
+    - name: --GC_depth
+      type: double
+      description: |
+        The size of GC-depth bins (decreasing bin size increases memory requirement).
+      default: 20000.0
+    - name: --insert_size
+      alternatives: -i
+      type: integer
+      description: |
+        Maximum insert size.
+      default: 8000
+    - name: --id
+      alternatives: -I
+      type: string
+      description: |
+        Include only listed read group or sample name.
+    - name: --read_length
+      alternatives: -l
+      type: integer
+      description: |
+        Include in the statistics only reads with the given read length.
+      default: -1
+    - name: --most_inserts
+      alternatives: -m
+      type: double
+      description: |
+        Report only the main part of inserts.
+      default: 0.99
+    - name: --split_prefix
+      alternatives: -P
+      type: string
+      description: |
+        Path or string prefix for filepaths output by --split (default is input filename).
+    - name: --trim_quality
+      alternatives: -q
+      type: integer
+      description: |
+        The BWA trimming parameter.
+      default: 0
+    - name: --ref_seq
+      alternatives: -r
+      type: file
+      description: |
+        Reference sequence (required for GC-depth and mismatches-per-cycle calculation).
+    - name: --split
+      alternatives: -S
+      type: string
+      description: |
+        Also write statistics to separate files split by tagged field.
+    - name: --target_regions
+      alternatives: -t
+      type: file
+      description: |
+        Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.
+    - name: --sparse
+      alternatives: -x
+      type: boolean_true
+      description: |
+        Suppress outputting IS rows where there are no insertions.
+    - name: --remove_overlaps
+      alternatives: -p
+      type: boolean_true
+      description: |
+        Remove overlaps of paired-end reads from coverage and base count computations.
+    - name: --cov_threshold
+      alternatives: -g
+      type: integer
+      description: |
+        Only bases with coverage above this value will be included in the target percentage computation.
+      default: 0
+    - name: --input_fmt_option
+      type: string
+      description: |
+        Specify a single input file format option in the form of OPTION or OPTION=VALUE.
+    - name: --reference
+      type: file
+      description: |
+        Reference sequence FASTA FILE.
+  - name: Outputs
+    arguments:
+    - name: --output
+      alternatives: -o
+      type: file
+      description: |
+        Output file.
+      default: "out.txt"
+      required: true
+      direction: output
+
+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/samtools:1.19.2--h50ea8bc_1
+    setup:
+      - type: docker
+        run: |
+          samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
+          sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
+runners:
+- type: executable
+- type: nextflow

src/samtools/samtools_stats/help.txt

@@ -0,0 +1,36 @@
+```
+samtools stats -h
+```
+
+Usage: samtools stats [OPTIONS] file.bam
+       samtools stats [OPTIONS] file.bam chr:from-to
+Options:
+    -c, --coverage <int>,<int>,<int>    Coverage distribution min,max,step [1,1000,1]
+    -d, --remove-dups                   Exclude from statistics reads marked as duplicates
+    -X, --customized-index-file         Use a customized index file
+    -f, --required-flag  <str|int>      Required flag, 0 for unset. See also `samtools flags` [0]
+    -F, --filtering-flag <str|int>      Filtering flag, 0 for unset. See also `samtools flags` [0]
+        --GC-depth <float>              the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]
+    -h, --help                          This help message
+    -i, --insert-size <int>             Maximum insert size [8000]
+    -I, --id <string>                   Include only listed read group or sample name
+    -l, --read-length <int>             Include in the statistics only reads with the given read length [-1]
+    -m, --most-inserts <float>          Report only the main part of inserts [0.99]
+    -P, --split-prefix <str>            Path or string prefix for filepaths output by -S (default is input filename)
+    -q, --trim-quality <int>            The BWA trimming parameter [0]
+    -r, --ref-seq <file>                Reference sequence (required for GC-depth and mismatches-per-cycle calculation).
+    -s, --sam                           Ignored (input format is auto-detected).
+    -S, --split <tag>                   Also write statistics to separate files split by tagged field.
+    -t, --target-regions <file>         Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.
+    -x, --sparse                        Suppress outputting IS rows where there are no insertions.
+    -p, --remove-overlaps               Remove overlaps of paired-end reads from coverage and base count computations.
+    -g, --cov-threshold <int>           Only bases with coverage above this value will be included in the target percentage computation [0]
+      --input-fmt-option OPT[=VAL]
+               Specify a single input file format option in the form
+               of OPTION or OPTION=VALUE
+      --reference FILE
+               Reference sequence FASTA FILE [null]
+  -@, --threads INT
+               Number of additional threads to use [0]
+      --verbosity INT
+               Set level of verbosity

src/samtools/samtools_stats/script.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -e
+
+[[ "$par_remove_dups" == "false" ]] && unset par_remove_dups
+[[ "$par_customized_index_file" == "false" ]] && unset par_customized_index_file
+[[ "$par_sparse" == "false" ]] && unset par_sparse
+[[ "$par_remove_overlaps" == "false" ]] && unset par_remove_overlaps
+
+samtools stats \
+    ${par_coverage:+-c "$par_coverage"} \
+    ${par_remove_dups:+-d} \
+    ${par_required_flag:+-f "$par_required_flag"} \
+    ${par_filtering_flag:+-F "$par_filtering_flag"} \
+    ${par_GC_depth:+--GC-depth "$par_GC_depth"} \
+    ${par_insert_size:+-i "$par_insert_size"} \
+    ${par_id:+-I "$par_id"} \
+    ${par_read_length:+-l "$par_read_length"} \
+    ${par_most_inserts:+-m "$par_most_inserts"} \
+    ${par_split_prefix:+-P "$par_split_prefix"} \
+    ${par_trim_quality:+-q "$par_trim_quality"} \
+    ${par_ref_seq:+-r "$par_ref_seq"} \
+    ${par_split:+-S "$par_split"} \
+    ${par_target_regions:+-t "$par_target_regions"} \
+    ${par_sparse:+-x} \
+    ${par_remove_overlaps:+-p} \
+    ${par_cov_threshold:+-g "$par_cov_threshold"} \
+    ${par_input_fmt_option:+-O "$par_input_fmt_option"} \
+    ${par_reference:+-R "$par_reference"} \
+    "$par_input" \
+    > "$par_output"
+
+exit 0

src/samtools/samtools_stats/test.sh

@@ -0,0 +1,78 @@
+#!/bin/bash
+
+test_dir="${meta_resources_dir}/test_data"
+
+############################################################################################
+
+echo ">>> Test 1: $meta_functionality_name"
+"$meta_executable" \
+  --input "$test_dir/test.paired_end.sorted.bam" \
+  --bai "$test_dir/test.paired_end.sorted.bam.bai" \
+  --output "$test_dir/test.paired_end.sorted.txt"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$test_dir/test.paired_end.sorted.txt" ] && echo "File 'test.paired_end.sorted.txt' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$test_dir/test.paired_end.sorted.txt" ] && echo "File 'test.paired_end.sorted.txt' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+# compare using diff,  ignoring the line stating the command that was passed.
+diff <(grep -v "^# The command" "$test_dir/test.paired_end.sorted.txt") \
+    <(grep -v "^# The command" "$test_dir/ref.paired_end.sorted.txt") || \
+    (echo "Output file ref.paired_end.sorted.txt does not match expected output" && exit 1)
+
+rm "$test_dir/test.paired_end.sorted.txt"
+
+############################################################################################
+
+echo ">>> Test 2: $meta_functionality_name with --remove_dups"
+"$meta_executable" \
+  --remove_dups \
+  --input "$test_dir/test.paired_end.sorted.bam" \
+  --bai "$test_dir/test.paired_end.sorted.bam.bai" \
+  --output "$test_dir/test.d.paired_end.sorted.txt"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$test_dir/ref.d.paired_end.sorted.txt" ] && echo "File 'ref.d.paired_end.sorted.txt' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$test_dir/ref.d.paired_end.sorted.txt" ] && echo "File 'ref.d.paired_end.sorted.txt' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+# compare using diff, ignoring the line stating the command that was passed.
+diff <(grep -v "^# The command" "$test_dir/test.d.paired_end.sorted.txt") \
+    <(grep -v "^# The command" "$test_dir/ref.d.paired_end.sorted.txt") || \
+    (echo "Output file ref.d.paired_end.sorted.txt does not match expected output" && exit 1)
+
+rm "$test_dir/test.d.paired_end.sorted.txt"
+
+############################################################################################
+
+echo ">>> Test 3: $meta_functionality_name with --remove_overlaps"
+"$meta_executable" \
+  --remove_overlaps \
+  --input "$test_dir/test.paired_end.sorted.bam" \
+  --bai "$test_dir/test.paired_end.sorted.bam.bai" \
+  --output "$test_dir/test.p.paired_end.sorted.txt" 
+
+echo ">>> Checking whether output exists"
+[ ! -f "$test_dir/ref.p.paired_end.sorted.txt" ] && echo "File 'ref.p.paired_end.sorted.txt' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$test_dir/ref.p.paired_end.sorted.txt" ] && echo "File 'ref.p.paired_end.sorted.txt' is empty!" && exit 1
+
+
+echo ">>> Checking whether output is correct"
+# compare using diff, ignoring the line stating the command that was passed.
+diff <(grep -v "^# The command" "$test_dir/test.p.paired_end.sorted.txt") \
+    <(grep -v "^# The command" "$test_dir/ref.p.paired_end.sorted.txt") || \
+    (echo "Output file ref.p.paired_end.sorted.txt does not match expected output" && exit 1)
+
+rm "$test_dir/test.p.paired_end.sorted.txt"
+
+############################################################################################
+
+echo ">>> All tests passed successfully."
+
+exit 0