From d0e37cdc3b3a38b27f55f2e10b7879161e78eef1 Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Fri, 29 Mar 2024 14:11:00 +0100
Subject: [PATCH] idxstats component

---
 CHANGELOG.md                                  |   3 +
 src/samtools/idxstats/config.vsh.yaml         |  52 ++++++++++++++++++
 src/samtools/idxstats/help.txt                |   5 ++
 src/samtools/idxstats/script.sh               |   8 +++
 src/samtools/idxstats/test.sh                 |  51 +++++++++++++++++
 src/samtools/idxstats/test_data/a.sorted.bam  | Bin 0 -> 209 bytes
 .../idxstats/test_data/a.sorted.bam.bai       | Bin 0 -> 96 bytes
 .../idxstats/test_data/a_ref.sorted.idxstats  |   2 +
 src/samtools/idxstats/test_data/script.sh     |  14 +++++
 .../test_data/test.paired_end.sorted.bam      | Bin 0 -> 19725 bytes
 .../test_data/test.paired_end.sorted.bam.bai  | Bin 0 -> 128 bytes
 .../test_ref.paired_end.sorted.idxstats       |   2 +
 12 files changed, 137 insertions(+)
 create mode 100644 src/samtools/idxstats/config.vsh.yaml
 create mode 100644 src/samtools/idxstats/help.txt
 create mode 100644 src/samtools/idxstats/script.sh
 create mode 100644 src/samtools/idxstats/test.sh
 create mode 100644 src/samtools/idxstats/test_data/a.sorted.bam
 create mode 100644 src/samtools/idxstats/test_data/a.sorted.bam.bai
 create mode 100644 src/samtools/idxstats/test_data/a_ref.sorted.idxstats
 create mode 100755 src/samtools/idxstats/test_data/script.sh
 create mode 100644 src/samtools/idxstats/test_data/test.paired_end.sorted.bam
 create mode 100644 src/samtools/idxstats/test_data/test.paired_end.sorted.bam.bai
 create mode 100644 src/samtools/idxstats/test_data/test_ref.paired_end.sorted.idxstats

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c3f22e96..16d0eaed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -35,6 +35,9 @@
     - `salmon/salmon_index`: Create a salmon index for the transcriptome to use Salmon in the mapping-based mode (PR #24).
     - `salmon/salmon_quant`: Transcript quantification from RNA-seq data (PR #24).
 
+* `samtools`:
+    - `samtools/idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
+
 ## MAJOR CHANGES
 
 ## MINOR CHANGES
diff --git a/src/samtools/idxstats/config.vsh.yaml b/src/samtools/idxstats/config.vsh.yaml
new file mode 100644
index 00000000..daab15be
--- /dev/null
+++ b/src/samtools/idxstats/config.vsh.yaml
@@ -0,0 +1,52 @@
+name: samtools_idxstats
+namespace: samtools
+description: Reports alignment summary statistics for a BAM file
+keywords: [stats, mapping, counts, chromosome, bam, sam, cram]
+links:
+  homepage: https://www.htslib.org/
+  documentation: https://www.htslib.org/doc/samtools-idxstats.html
+  repository: https://github.com/samtools/samtools.git
+references: 
+  doi: 10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008
+license: MIT/Expat
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: "--bam"
+        type: file
+        description: BAM input file.
+      - name: "--bai"
+        type: file
+        description: BAM index file.
+      - name: "--fasta"
+        type: file
+        description: Reference file the CRAM was created with (optional).
+  - name: Outputs
+    arguments:
+      - name: "--output"
+        type: file
+        description: |
+          File containing samtools stats output in tab-delimited format.
+        required: true
+        must_exist: false
+        example: output.idxstats
+   
+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:1.3.1--h9071d68_10
+    setup:
+      - type: docker
+        run: |
+          echo "$(samtools --version 2>&1)" > /var/software_versions.txt
+runners:
+- type: executable
+- type: nextflow
\ No newline at end of file
diff --git a/src/samtools/idxstats/help.txt b/src/samtools/idxstats/help.txt
new file mode 100644
index 00000000..c0fb5947
--- /dev/null
+++ b/src/samtools/idxstats/help.txt
@@ -0,0 +1,5 @@
+```
+samtools idxstats
+```
+
+Usage: samtools idxstats <in.bam>
\ No newline at end of file
diff --git a/src/samtools/idxstats/script.sh b/src/samtools/idxstats/script.sh
new file mode 100644
index 00000000..9f8d4af4
--- /dev/null
+++ b/src/samtools/idxstats/script.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -e
+
+samtools idxstats "$par_bam" > "$par_output"
\ No newline at end of file
diff --git a/src/samtools/idxstats/test.sh b/src/samtools/idxstats/test.sh
new file mode 100644
index 00000000..b66577e7
--- /dev/null
+++ b/src/samtools/idxstats/test.sh
@@ -0,0 +1,51 @@
+#!/bin/bash
+
+test_dir="${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 "$test_dir/a.sorted.idxstats"
+
+echo "$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
diff --git a/src/samtools/idxstats/test_data/a.sorted.bam b/src/samtools/idxstats/test_data/a.sorted.bam
new file mode 100644
index 0000000000000000000000000000000000000000..1c81d7cd59e70b71fce1ed9911445e08d1da7df8
GIT binary patch
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diff --git a/src/samtools/idxstats/test_data/a.sorted.bam.bai b/src/samtools/idxstats/test_data/a.sorted.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..4f08f5d5e5e01de5042cb8f625c1d26b338c3394
GIT binary patch
literal 96
vcmZ>A^kigYU|?VZVoxCk1`wNpAp%S?Fl+_WUXvj5=;CZpRWJ%wFGLgo8^r{K

literal 0
HcmV?d00001

diff --git a/src/samtools/idxstats/test_data/a_ref.sorted.idxstats b/src/samtools/idxstats/test_data/a_ref.sorted.idxstats
new file mode 100644
index 00000000..27862419
--- /dev/null
+++ b/src/samtools/idxstats/test_data/a_ref.sorted.idxstats
@@ -0,0 +1,2 @@
+xx	20	6	0
+*	0	0	0
diff --git a/src/samtools/idxstats/test_data/script.sh b/src/samtools/idxstats/test_data/script.sh
new file mode 100755
index 00000000..0e28a4c6
--- /dev/null
+++ b/src/samtools/idxstats/test_data/script.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# dowload test data from snakemake wrapper
+if [ ! -d /tmp/idxstats_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers.git /tmp/idxstats_source
+fi
+
+cp -r /tmp/idxstats_source/bio/samtools/idxstats/test/mapped/* src/samtools/idxstats/test_data
+# samtools idxstats a.sorted.bam > a.sorted.idxstats
+
+# dowload test data from nf-core module
+wget https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam
+wget https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai
+# samtools idxstats test.paired_end.sorted.bam > test_ref.paired_end.sorted.idxstats
\ No newline at end of file
diff --git a/src/samtools/idxstats/test_data/test.paired_end.sorted.bam b/src/samtools/idxstats/test_data/test.paired_end.sorted.bam
new file mode 100644
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diff --git a/src/samtools/idxstats/test_data/test_ref.paired_end.sorted.idxstats b/src/samtools/idxstats/test_data/test_ref.paired_end.sorted.idxstats
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