From 2433679cae4a1762db0406e37a6a2d2a9663b235 Mon Sep 17 00:00:00 2001
From: Hendrik Cannoodt <hendrik.cannoodt@gmail.com>
Date: Wed, 3 Apr 2024 17:12:19 +0200
Subject: [PATCH 1/2] Fix missing slash in path construction (#34)

* Fix missing slash in path construction

* add one more

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
---
 src/gffread/test.sh                    | 8 ++++----
 src/samtools/samtools_flagstat/test.sh | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/gffread/test.sh b/src/gffread/test.sh
index 6d38012b..326fce50 100755
--- a/src/gffread/test.sh
+++ b/src/gffread/test.sh
@@ -5,9 +5,9 @@
 
 set -e
 
-test_output_dir="${meta_resources_dir}test_data/test_output"
-test_dir="${meta_resources_dir}test_data"
-expected_output_dir="${meta_resources_dir}test_data/output"
+test_output_dir="${meta_resources_dir}/test_data/test_output"
+test_dir="${meta_resources_dir}/test_data"
+expected_output_dir="${meta_resources_dir}/test_data/output"
 
 mkdir -p "$test_output_dir"
 
@@ -108,4 +108,4 @@ rm -r "$test_output_dir"
 
 echo "> All tests successful"
 
-exit 0
\ No newline at end of file
+exit 0
diff --git a/src/samtools/samtools_flagstat/test.sh b/src/samtools/samtools_flagstat/test.sh
index ec5a5b07..647c64af 100644
--- a/src/samtools/samtools_flagstat/test.sh
+++ b/src/samtools/samtools_flagstat/test.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-test_dir="${meta_resources_dir}test_data"
+test_dir="${meta_resources_dir}/test_data"
 echo ">>> Testing $meta_functionality_name"
 
 "$meta_executable" \

From 1200bc37611974a095b53c130cb34dc3286a931f Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Wed, 3 Apr 2024 17:12:51 +0200
Subject: [PATCH 2/2] Samtools idxstats component (#32)

* idxstats component

* Update samtools version

* Apply suggestions for PR

* Update src/samtools/samtools_idxstats/test.sh

Add a slash to path to test data

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
---
 CHANGELOG.md                                  |   2 +-
 .../samtools_idxstats/config.vsh.yaml         |  53 ++++++++++++++++++
 src/samtools/samtools_idxstats/help.txt       |  12 ++++
 src/samtools/samtools_idxstats/script.sh      |   8 +++
 src/samtools/samtools_idxstats/test.sh        |  49 ++++++++++++++++
 .../samtools_idxstats/test_data/a.sorted.bam  | Bin 0 -> 209 bytes
 .../test_data/a.sorted.bam.bai                | Bin 0 -> 96 bytes
 .../test_data/a_ref.sorted.idxstats           |   2 +
 .../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, 141 insertions(+), 1 deletion(-)
 create mode 100644 src/samtools/samtools_idxstats/config.vsh.yaml
 create mode 100644 src/samtools/samtools_idxstats/help.txt
 create mode 100644 src/samtools/samtools_idxstats/script.sh
 create mode 100644 src/samtools/samtools_idxstats/test.sh
 create mode 100644 src/samtools/samtools_idxstats/test_data/a.sorted.bam
 create mode 100644 src/samtools/samtools_idxstats/test_data/a.sorted.bam.bai
 create mode 100644 src/samtools/samtools_idxstats/test_data/a_ref.sorted.idxstats
 create mode 100755 src/samtools/samtools_idxstats/test_data/script.sh
 create mode 100644 src/samtools/samtools_idxstats/test_data/test.paired_end.sorted.bam
 create mode 100644 src/samtools/samtools_idxstats/test_data/test.paired_end.sorted.bam.bai
 create mode 100644 src/samtools/samtools_idxstats/test_data/test_ref.paired_end.sorted.idxstats

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c3a0a398..4fd7f001 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,7 +37,7 @@
 
 * `samtools`:
     - `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).
 
 ## MAJOR CHANGES
 
diff --git a/src/samtools/samtools_idxstats/config.vsh.yaml b/src/samtools/samtools_idxstats/config.vsh.yaml
new file mode 100644
index 00000000..781bd8be
--- /dev/null
+++ b/src/samtools/samtools_idxstats/config.vsh.yaml
@@ -0,0 +1,53 @@
+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
+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:1.19.2--h50ea8bc_1
+    setup:
+      - type: docker
+        run: |
+          samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
+          sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
+runners:
+- type: executable
+- type: nextflow
\ No newline at end of file
diff --git a/src/samtools/samtools_idxstats/help.txt b/src/samtools/samtools_idxstats/help.txt
new file mode 100644
index 00000000..7b63ab17
--- /dev/null
+++ b/src/samtools/samtools_idxstats/help.txt
@@ -0,0 +1,12 @@
+```
+samtools idxstats
+```
+
+Usage: samtools idxstats [options] <in.bam>
+      --input-fmt-option OPT[=VAL]
+               Specify a single input file format option in the form
+               of OPTION or OPTION=VALUE
+  -@, --threads INT
+               Number of additional threads to use [0]
+      --verbosity INT
+               Set level of verbosity
\ No newline at end of file
diff --git a/src/samtools/samtools_idxstats/script.sh b/src/samtools/samtools_idxstats/script.sh
new file mode 100644
index 00000000..9f8d4af4
--- /dev/null
+++ b/src/samtools/samtools_idxstats/script.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -e
+
+samtools idxstats "$par_bam" > "$par_output"
\ No newline at end of file
diff --git a/src/samtools/samtools_idxstats/test.sh b/src/samtools/samtools_idxstats/test.sh
new file mode 100644
index 00000000..1459ec08
--- /dev/null
+++ b/src/samtools/samtools_idxstats/test.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+test_dir="${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
diff --git a/src/samtools/samtools_idxstats/test_data/a.sorted.bam b/src/samtools/samtools_idxstats/test_data/a.sorted.bam
new file mode 100644
index 0000000000000000000000000000000000000000..1c81d7cd59e70b71fce1ed9911445e08d1da7df8
GIT binary patch
literal 209
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literal 0
HcmV?d00001

diff --git a/src/samtools/samtools_idxstats/test_data/a.sorted.bam.bai b/src/samtools/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/samtools_idxstats/test_data/a_ref.sorted.idxstats b/src/samtools/samtools_idxstats/test_data/a_ref.sorted.idxstats
new file mode 100644
index 00000000..27862419
--- /dev/null
+++ b/src/samtools/samtools_idxstats/test_data/a_ref.sorted.idxstats
@@ -0,0 +1,2 @@
+xx	20	6	0
+*	0	0	0
diff --git a/src/samtools/samtools_idxstats/test_data/script.sh b/src/samtools/samtools_idxstats/test_data/script.sh
new file mode 100755
index 00000000..0e28a4c6
--- /dev/null
+++ b/src/samtools/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/samtools_idxstats/test_data/test.paired_end.sorted.bam b/src/samtools/samtools_idxstats/test_data/test.paired_end.sorted.bam
new file mode 100644
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diff --git a/src/samtools/samtools_idxstats/test_data/test_ref.paired_end.sorted.idxstats b/src/samtools/samtools_idxstats/test_data/test_ref.paired_end.sorted.idxstats
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