From 725614c1729e912e8de1b7c91df3709c9294e256 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Wed, 21 Aug 2024 09:09:04 +0200
Subject: [PATCH 01/21] Use datadir to discover testfiles

---
 GenderCheck/test_calculate_gender.py          |  26 ++++++++++--------
 .../{ => test_calculate_gender}/test_bam.bam  | Bin
 .../test_bam.bam.bai                          | Bin
 .../1.0.0/test_get_gender_from_bam_chrx.py    |  22 ++++++++-------
 .../test_bam.bam                              | Bin
 .../test_bam.bam.bai                          | Bin
 6 files changed, 27 insertions(+), 21 deletions(-)
 rename GenderCheck/{ => test_calculate_gender}/test_bam.bam (100%)
 rename GenderCheck/{ => test_calculate_gender}/test_bam.bam.bai (100%)
 rename MosaicHunter/1.0.0/{ => test_get_gender_from_bam_chrx}/test_bam.bam (100%)
 rename MosaicHunter/1.0.0/{ => test_get_gender_from_bam_chrx}/test_bam.bam.bai (100%)

diff --git a/GenderCheck/test_calculate_gender.py b/GenderCheck/test_calculate_gender.py
index 500e9c8..27a0bb3 100644
--- a/GenderCheck/test_calculate_gender.py
+++ b/GenderCheck/test_calculate_gender.py
@@ -1,7 +1,11 @@
-import calculate_gender
-
+#!/usr/bin/env python
+# Import statements, alphabetic order of main package.
+# Third party libraries alphabetic order of main package.
 import pytest
 
+# Custom libraries alphabetic order of main package.
+import calculate_gender
+
 
 class TestIsValidRead():
 
@@ -12,11 +16,11 @@ def __init__(self, qual, start, end):
             self.reference_end = end
 
     @pytest.mark.parametrize("read,mapping_qual,expected", [
-        (MyObject(19, True, True), 20, False),  # mapping quality is below the threshold
-        (MyObject(20, True, True), 20, True),  # mapping quality is equal to the threshold
-        (MyObject(20, True, True), 19, True),  # mapping quality is higher than the threshold
-        (MyObject(20, False, True), 20, False),  # reference_end is false
-        (MyObject(20, True, False), 20, False),  # reference_start is false
+        (MyObject(19, True, True), 20, False),  # Mapping quality is below the threshold
+        (MyObject(20, True, True), 20, True),  # Mapping quality is equal to the threshold
+        (MyObject(20, True, True), 19, True),  # Mapping quality is higher than the threshold
+        (MyObject(20, False, True), 20, False),  # Reference_end is false
+        (MyObject(20, True, False), 20, False),  # Reference_start is false
     ])
     def test_is_valid_read(self, read, mapping_qual, expected):
         assert expected == calculate_gender.is_valid_read(read, mapping_qual)
@@ -24,11 +28,11 @@ def test_is_valid_read(self, read, mapping_qual, expected):
 
 class TestGetGenderFromBam():
     @pytest.mark.parametrize("bam,mapping_qual,locus_y,ratio_y,expected", [
-        ("./test_bam.bam", 20, "Y:2649520-59034050", 0.02, "male"),  # output male below
-        ("./test_bam.bam", 20, "Y:2649520-59034050", 0.22, "female"),  # output female
+        ("test_bam.bam", 20, "Y:2649520-59034050", 0.02, "male"),  # Output male below
+        ("test_bam.bam", 20, "Y:2649520-59034050", 0.22, "female"),  # Output female
     ])
-    def test_get_gender_from_bam(self, bam, mapping_qual, locus_y, ratio_y, expected):
-        assert expected == calculate_gender.get_gender_from_bam(bam, mapping_qual, locus_y, ratio_y)
+    def test_get_gender_from_bam(self, bam, mapping_qual, locus_y, ratio_y, expected, datadir):
+        assert expected == calculate_gender.get_gender_from_bam(f"{datadir}/{bam}", mapping_qual, locus_y, ratio_y)
 
 
 class TestCompareGender():
diff --git a/GenderCheck/test_bam.bam b/GenderCheck/test_calculate_gender/test_bam.bam
similarity index 100%
rename from GenderCheck/test_bam.bam
rename to GenderCheck/test_calculate_gender/test_bam.bam
diff --git a/GenderCheck/test_bam.bam.bai b/GenderCheck/test_calculate_gender/test_bam.bam.bai
similarity index 100%
rename from GenderCheck/test_bam.bam.bai
rename to GenderCheck/test_calculate_gender/test_bam.bam.bai
diff --git a/MosaicHunter/1.0.0/test_get_gender_from_bam_chrx.py b/MosaicHunter/1.0.0/test_get_gender_from_bam_chrx.py
index 0a494ea..a3fa47a 100644
--- a/MosaicHunter/1.0.0/test_get_gender_from_bam_chrx.py
+++ b/MosaicHunter/1.0.0/test_get_gender_from_bam_chrx.py
@@ -10,11 +10,11 @@ def __init__(self, qual, start, end):
             self.reference_end = end
 
     @pytest.mark.parametrize("read,mapping_qual,expected", [
-        (ValidReadObject(19, True, True), 20, False),  # mapping quality is below the threshold
-        (ValidReadObject(20, True, True), 20, True),  # mapping quality is equal to the threshold
-        (ValidReadObject(20, True, True), 19, True),  # mapping quality is higher than the threshold
-        (ValidReadObject(20, False, True), 20, False),  # reference_end is false
-        (ValidReadObject(20, True, False), 20, False),  # reference_start is false
+        (ValidReadObject(19, True, True), 20, False),  # Mapping quality is below the threshold
+        (ValidReadObject(20, True, True), 20, True),  # Mapping quality is equal to the threshold
+        (ValidReadObject(20, True, True), 19, True),  # Mapping quality is higher than the threshold
+        (ValidReadObject(20, False, True), 20, False),  # Reference_end is false
+        (ValidReadObject(20, True, False), 20, False),  # Reference_start is false
     ])
     def test_is_valid_read(self, read, mapping_qual, expected):
         assert expected == get_gender_from_bam_chrx.is_valid_read(read, mapping_qual)
@@ -22,13 +22,15 @@ def test_is_valid_read(self, read, mapping_qual, expected):
 
 class TestGetGenderFromBam:
     @pytest.mark.parametrize("bam,mapping_qual,locus_x,ratio_x_threshold_male,ratio_x_threshold_female,expected_outcome", [
-        ("./test_bam.bam", 20, "X:2699520-154931044", 3.5, 4.5, ("F", False)),
-        ("./test_bam.bam", 20, "X:2699520-154931044", 5.5, 7.5, ("M", False)),
-        ("./test_bam.bam", 20, "X:2699520-154931044", 4.5, 6.5, ("F", True)),
+        ("test_bam.bam", 20, "X:2699520-154931044", 3.5, 4.5, ("F", False)),
+        ("test_bam.bam", 20, "X:2699520-154931044", 5.5, 7.5, ("M", False)),
+        ("test_bam.bam", 20, "X:2699520-154931044", 4.5, 6.5, ("F", True)),
     ])
-    def test_get_gender_from_bam(self, bam, mapping_qual, locus_x, ratio_x_threshold_male, ratio_x_threshold_female, expected_outcome):
+    def test_get_gender_from_bam(
+        self, bam, mapping_qual, locus_x, ratio_x_threshold_male, ratio_x_threshold_female, expected_outcome, datadir
+    ):
         assert expected_outcome == get_gender_from_bam_chrx.get_gender_from_bam_chrx(
-            bam, mapping_qual, locus_x, ratio_x_threshold_male, ratio_x_threshold_female)
+            f"{datadir}/{bam}", mapping_qual, locus_x, ratio_x_threshold_male, ratio_x_threshold_female)
 
 
 class TestWriteGenderDataToFile:
diff --git a/MosaicHunter/1.0.0/test_bam.bam b/MosaicHunter/1.0.0/test_get_gender_from_bam_chrx/test_bam.bam
similarity index 100%
rename from MosaicHunter/1.0.0/test_bam.bam
rename to MosaicHunter/1.0.0/test_get_gender_from_bam_chrx/test_bam.bam
diff --git a/MosaicHunter/1.0.0/test_bam.bam.bai b/MosaicHunter/1.0.0/test_get_gender_from_bam_chrx/test_bam.bam.bai
similarity index 100%
rename from MosaicHunter/1.0.0/test_bam.bam.bai
rename to MosaicHunter/1.0.0/test_get_gender_from_bam_chrx/test_bam.bam.bai

From b7e73dd2d52fcff288fe5bc98b52810ddbb7803f Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Wed, 21 Aug 2024 09:10:52 +0200
Subject: [PATCH 02/21] Resolve flake8 warnings and errors

---
 Utils/create_hsmetrics_summary.py |  2 +-
 Utils/get_stats_from_flagstat.py  | 26 ++++++++++++++++++++------
 2 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/Utils/create_hsmetrics_summary.py b/Utils/create_hsmetrics_summary.py
index 405e1ce..4256fc3 100644
--- a/Utils/create_hsmetrics_summary.py
+++ b/Utils/create_hsmetrics_summary.py
@@ -8,7 +8,7 @@
     parser.add_argument('hsmetrics_files', type=argparse.FileType('r'), nargs='*', help='HSMetric file')
     arguments = parser.parse_args()
 
-    interval_files_pattern = re.compile("BAIT_INTERVALS=\[(\S*)\].TARGET_INTERVALS=\[(\S*)\]")
+    interval_files_pattern = re.compile("BAIT_INTERVALS=\[(\S*)\].TARGET_INTERVALS=\[(\S*)\]")  # noqa: W605
     summary_header = []
     summary_data = {}
     for hsmetrics_file in arguments.hsmetrics_files:
diff --git a/Utils/get_stats_from_flagstat.py b/Utils/get_stats_from_flagstat.py
index 2f46abb..75a145a 100644
--- a/Utils/get_stats_from_flagstat.py
+++ b/Utils/get_stats_from_flagstat.py
@@ -43,12 +43,26 @@
 
         print("\n\t{0} %duplication\n".format(100*sample_dups/sample_mapped))
 
-    print("Total raw reads: {total:,} reads (Total throughput, 75bp={total_75bp:,} bp, 100bp={total_100bp:,} bp, 150bp={total_150bp:,} bp)".format(
-        total=counts['total'], total_75bp=counts['total']*75, total_100bp=counts['total']*100, total_150bp=counts['total']*150
-    ))
-    print("Total mapped reads: {total:,} reads (Total throughput, 75bp={total_75bp:,} bp, 100bp={total_100bp:,} bp, 150bp={total_150bp:,} bp)".format(
-        total=counts['mapped'], total_75bp=counts['mapped']*75, total_100bp=counts['mapped']*100, total_150bp=counts['mapped']*150
-    ))
+    print(
+        "Total raw reads: {total:,} reads "
+        "(Total throughput, 75bp={total_75bp:,} bp, 100bp={total_100bp:,} bp, 150bp={total_150bp:,} bp)".format(
+            total=counts['total'],
+            total_75bp=counts['total']*75,
+            total_100bp=counts['total']*100,
+            total_150bp=counts['total']*150
+        )
+    )
+
+    print(
+        "Total mapped reads: {total:,} reads "
+        "(Total throughput, 75bp={total_75bp:,} bp, 100bp={total_100bp:,} bp, 150bp={total_150bp:,} bp)"
+        .format(
+            total=counts['mapped'],
+            total_75bp=counts['mapped']*75,
+            total_100bp=counts['mapped']*100,
+            total_150bp=counts['mapped']*150
+        )
+    )
     print("Average mapped per lib: {:,} reads".format(int(round(float(counts['mapped'])/float(counts['files'])))))
     print("Average dups per lib: {:,} reads".format(int(round(float(counts['dups'])/float(counts['files'])))))
     print("Average dups % per lib: {:.2f} %".format(100*float(counts['dups'])/float(counts['mapped'])))

From 07bc221cfdcc2cab5e7654b21442214ac62e1c78 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Tue, 17 Sep 2024 13:39:10 +0200
Subject: [PATCH 03/21] add checkqc github action

---
 .github/workflows/checkqc_lint.yml |   8 +
 .github/workflows/checkqc_test.yml |  54 +++
 CheckQC/poetry.lock                | 686 +++++++++++++++++++++++++++++
 CheckQC/pyproject.toml             |  32 ++
 4 files changed, 780 insertions(+)
 create mode 100644 .github/workflows/checkqc_lint.yml
 create mode 100644 .github/workflows/checkqc_test.yml
 create mode 100644 CheckQC/poetry.lock
 create mode 100644 CheckQC/pyproject.toml

diff --git a/.github/workflows/checkqc_lint.yml b/.github/workflows/checkqc_lint.yml
new file mode 100644
index 0000000..690db14
--- /dev/null
+++ b/.github/workflows/checkqc_lint.yml
@@ -0,0 +1,8 @@
+name: CheckQC Lint
+on: pull_request
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/checkqc_test.yml b/.github/workflows/checkqc_test.yml
new file mode 100644
index 0000000..48081c9
--- /dev/null
+++ b/.github/workflows/checkqc_test.yml
@@ -0,0 +1,54 @@
+# Source: https://github.com/marketplace/actions/install-poetry-action
+name: CheckQC Test
+on: pull_request
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+      #----------------------------------------------
+      # check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up python
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11.5'
+      #----------------------------------------------
+      # install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      #----------------------------------------------
+      # load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv_checkqc
+          key: venv_checkqc-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+      #----------------------------------------------
+      # install root project
+      #----------------------------------------------
+      - name: Install project
+        run: poetry install --no-interaction
+      #----------------------------------------------
+      # run pytest
+      #----------------------------------------------
+      - name: Run tests
+        run: |
+          source .venv_checkqc/bin/activate
+          pytest tests
diff --git a/CheckQC/poetry.lock b/CheckQC/poetry.lock
new file mode 100644
index 0000000..32eebbf
--- /dev/null
+++ b/CheckQC/poetry.lock
@@ -0,0 +1,686 @@
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+
+[[package]]
+name = "atomicwrites"
+version = "1.4.1"
+description = "Atomic file writes."
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
+]
+
+[[package]]
+name = "attrs"
+version = "24.2.0"
+description = "Classes Without Boilerplate"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
+    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
+]
+
+[package.extras]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+description = "Cross-platform colored terminal text."
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
+]
+
+[[package]]
+name = "coverage"
+version = "7.6.1"
+description = "Code coverage measurement for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "coverage-7.6.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b06079abebbc0e89e6163b8e8f0e16270124c154dc6e4a47b413dd538859af16"},
+    {file = "coverage-7.6.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:cf4b19715bccd7ee27b6b120e7e9dd56037b9c0681dcc1adc9ba9db3d417fa36"},
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+    {file = "coverage-7.6.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8f59d57baca39b32db42b83b2a7ba6f47ad9c394ec2076b084c3f029b7afca23"},
+    {file = "coverage-7.6.1-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:a1ac0ae2b8bd743b88ed0502544847c3053d7171a3cff9228af618a068ed9c34"},
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+    {file = "coverage-7.6.1-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:f5796e664fe802da4f57a168c85359a8fbf3eab5e55cd4e4569fbacecc903959"},
+    {file = "coverage-7.6.1-cp310-cp310-win32.whl", hash = "sha256:7bb65125fcbef8d989fa1dd0e8a060999497629ca5b0efbca209588a73356232"},
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+]
+
+[[package]]
+name = "six"
+version = "1.16.0"
+description = "Python 2 and 3 compatibility utilities"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
+    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
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+]
+
+[[package]]
+name = "toml"
+version = "0.10.2"
+description = "Python Library for Tom's Obvious, Minimal Language"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
+    {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
+    {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
+]
+
+[[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+]
+
+[[package]]
+name = "tzdata"
+version = "2024.1"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+files = [
+    {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
+    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
+]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "3.9.2"
+content-hash = "64302a36da3450260a740f2ba7b94069fb90da4a5fe77cf3a8727c46f8c99d97"
diff --git a/CheckQC/pyproject.toml b/CheckQC/pyproject.toml
new file mode 100644
index 0000000..7652a75
--- /dev/null
+++ b/CheckQC/pyproject.toml
@@ -0,0 +1,32 @@
+[tool.poetry]
+name = "checkqc"
+version = "0.1.0"
+description = "Check and judge qc metrics (files)"
+authors = ["Your Name <you@example.com>"]
+license = 'MIT'
+package-mode = false
+
+[tool.poetry.dependencies]
+python = "3.9.2"
+pandas = "2.1.4"
+pyyaml = "6.0.1"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "6.2.5"
+pytest-cov = "3.0.0"
+pytest-datadir = "1.5.0"
+pytest-datafiles = "2.0"
+pytest-dataset = "0.3.2"
+pytest-flake8 = "1.0.7"
+pytest-mock = "3.8.2"
+pytest-raises = "0.11"
+pytest-reqs = "0.2.1"
+pytest-unordered = "0.5.2"
+
+[tool.ruff]
+line-length = 127
+indent-width = 4
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

From 3a2ed7167786bc3bee69fc0d09fb4a520cdb1685 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Wed, 18 Sep 2024 13:20:55 +0200
Subject: [PATCH 04/21] change poetry venv, and use working directory

---
 .github/workflows/checkqc_test.yml |  7 ++-
 CheckQC/poetry.lock                | 79 +++++-------------------------
 CheckQC/pyproject.toml             |  5 +-
 3 files changed, 20 insertions(+), 71 deletions(-)

diff --git a/.github/workflows/checkqc_test.yml b/.github/workflows/checkqc_test.yml
index 48081c9..b2a1b58 100644
--- a/.github/workflows/checkqc_test.yml
+++ b/.github/workflows/checkqc_test.yml
@@ -4,6 +4,9 @@ on: pull_request
 jobs:
   pytest:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./CheckQC/
     steps:
       #----------------------------------------------
       # check-out repo and set-up python
@@ -32,7 +35,7 @@ jobs:
         id: cached-poetry-dependencies
         uses: actions/cache@v4
         with:
-          path: .venv_checkqc
+          path: .venv
           key: venv_checkqc-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
       #----------------------------------------------
       # install dependencies if cache does not exist
@@ -50,5 +53,5 @@ jobs:
       #----------------------------------------------
       - name: Run tests
         run: |
-          source .venv_checkqc/bin/activate
+          source .venv/bin/activate
           pytest tests
diff --git a/CheckQC/poetry.lock b/CheckQC/poetry.lock
index 32eebbf..8b10920 100644
--- a/CheckQC/poetry.lock
+++ b/CheckQC/poetry.lock
@@ -1,34 +1,5 @@
 # This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
-[[package]]
-name = "atomicwrites"
-version = "1.4.1"
-description = "Atomic file writes."
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
-]
-
-[[package]]
-name = "attrs"
-version = "24.2.0"
-description = "Classes Without Boilerplate"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
-    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
-]
-
-[package.extras]
-benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
-tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
-
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -121,9 +92,6 @@ files = [
     {file = "coverage-7.6.1.tar.gz", hash = "sha256:953510dfb7b12ab69d20135a0662397f077c59b1e6379a768e97c59d852ee51d"},
 ]
 
-[package.dependencies]
-tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
-
 [package.extras]
 toml = ["tomli"]
 
@@ -256,7 +224,10 @@ files = [
 ]
 
 [package.dependencies]
-numpy = {version = ">=1.22.4,<2", markers = "python_version < \"3.11\""}
+numpy = [
+    {version = ">=1.23.2,<2", markers = "python_version == \"3.11\""},
+    {version = ">=1.26.0,<2", markers = "python_version >= \"3.12\""},
+]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
 tzdata = ">=2022.1"
@@ -388,27 +359,23 @@ files = [
 
 [[package]]
 name = "pytest"
-version = "6.2.5"
+version = "8.3.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "pytest-6.2.5-py3-none-any.whl", hash = "sha256:7310f8d27bc79ced999e760ca304d69f6ba6c6649c0b60fb0e04a4a77cacc134"},
-    {file = "pytest-6.2.5.tar.gz", hash = "sha256:131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89"},
+    {file = "pytest-8.3.3-py3-none-any.whl", hash = "sha256:a6853c7375b2663155079443d2e45de913a911a11d669df02a50814944db57b2"},
+    {file = "pytest-8.3.3.tar.gz", hash = "sha256:70b98107bd648308a7952b06e6ca9a50bc660be218d53c257cc1fc94fda10181"},
 ]
 
 [package.dependencies]
-atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
-attrs = ">=19.2.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
-py = ">=1.8.2"
-toml = "*"
+pluggy = ">=1.5,<2"
 
 [package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
@@ -647,28 +614,6 @@ files = [
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
 
-[[package]]
-name = "toml"
-version = "0.10.2"
-description = "Python Library for Tom's Obvious, Minimal Language"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-files = [
-    {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
-    {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
-]
-
-[[package]]
-name = "tomli"
-version = "2.0.1"
-description = "A lil' TOML parser"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
-]
-
 [[package]]
 name = "tzdata"
 version = "2024.1"
@@ -682,5 +627,5 @@ files = [
 
 [metadata]
 lock-version = "2.0"
-python-versions = "3.9.2"
-content-hash = "64302a36da3450260a740f2ba7b94069fb90da4a5fe77cf3a8727c46f8c99d97"
+python-versions = "^3.11.4"
+content-hash = "b9545131c195e37f949ffff6f6a065464f501b7922094a291b51a93cfc521886"
diff --git a/CheckQC/pyproject.toml b/CheckQC/pyproject.toml
index 7652a75..c7e7591 100644
--- a/CheckQC/pyproject.toml
+++ b/CheckQC/pyproject.toml
@@ -7,12 +7,13 @@ license = 'MIT'
 package-mode = false
 
 [tool.poetry.dependencies]
-python = "3.9.2"
+python = "^3.11.4"
 pandas = "2.1.4"
 pyyaml = "6.0.1"
+pytest = "^8.3.3"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "6.2.5"
+pytest = "^8.3.3"
 pytest-cov = "3.0.0"
 pytest-datadir = "1.5.0"
 pytest-datafiles = "2.0"

From b070824e6d8babe639fc3a7e405fd715d4213762 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Wed, 18 Sep 2024 13:33:55 +0200
Subject: [PATCH 05/21] add pyproject custommodules

---
 poetry.lock    | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++
 pyproject.toml | 19 +++++++++++++
 2 files changed, 93 insertions(+)
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml

diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..d886a2b
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,74 @@
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+description = "Cross-platform colored terminal text."
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
+]
+
+[[package]]
+name = "iniconfig"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
+
+[[package]]
+name = "packaging"
+version = "24.1"
+description = "Core utilities for Python packages"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "packaging-24.1-py3-none-any.whl", hash = "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"},
+    {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
+]
+
+[[package]]
+name = "pluggy"
+version = "1.5.0"
+description = "plugin and hook calling mechanisms for python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"},
+    {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"},
+]
+
+[package.extras]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
+
+[[package]]
+name = "pytest"
+version = "8.3.3"
+description = "pytest: simple powerful testing with Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pytest-8.3.3-py3-none-any.whl", hash = "sha256:a6853c7375b2663155079443d2e45de913a911a11d669df02a50814944db57b2"},
+    {file = "pytest-8.3.3.tar.gz", hash = "sha256:70b98107bd648308a7952b06e6ca9a50bc660be218d53c257cc1fc94fda10181"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=1.5,<2"
+
+[package.extras]
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.11.4"
+content-hash = "0e9c7de1a14ab89ba216b00deb52b83bda978915d965f459b3bfce8f2b6f5d77"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..a70546a
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,19 @@
+[tool.poetry]
+name = "custommodules"
+version = "0.1.0"
+description = "custom nextflow processes and their linked files"
+authors = ["Your Name <you@example.com>"]
+license = "MIT"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.11.4"
+pytest = "^8.3.3"
+
+[tool.ruff]
+line-length = 127
+indent-width = 4
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

From 856b46e5fa6d2b4732ce11777de806f13ef93e99 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 20 Sep 2024 08:57:29 +0200
Subject: [PATCH 06/21] run pytest in working dir

---
 .github/workflows/checkqc_test.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/checkqc_test.yml b/.github/workflows/checkqc_test.yml
index b2a1b58..6e48cc6 100644
--- a/.github/workflows/checkqc_test.yml
+++ b/.github/workflows/checkqc_test.yml
@@ -1,12 +1,15 @@
 # Source: https://github.com/marketplace/actions/install-poetry-action
 name: CheckQC Test
-on: pull_request
+on:
+  pull_request:
+    paths: CheckQC/**
+
 jobs:
   pytest:
     runs-on: ubuntu-latest
     defaults:
       run:
-        working-directory: ./CheckQC/
+        working-directory: CheckQC/
     steps:
       #----------------------------------------------
       # check-out repo and set-up python
@@ -54,4 +57,4 @@ jobs:
       - name: Run tests
         run: |
           source .venv/bin/activate
-          pytest tests
+          pytest .

From 52dc431e578730e0dd425c643fc0bb53a4370836 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 20 Sep 2024 09:06:49 +0200
Subject: [PATCH 07/21] Restrict github action checkqc lint to changes in path

---
 .github/workflows/checkqc_lint.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/checkqc_lint.yml b/.github/workflows/checkqc_lint.yml
index 690db14..94d80dc 100644
--- a/.github/workflows/checkqc_lint.yml
+++ b/.github/workflows/checkqc_lint.yml
@@ -1,5 +1,8 @@
 name: CheckQC Lint
-on: pull_request
+on:
+  pull_request:
+    paths: CheckQC/**
+
 jobs:
   ruff:
     runs-on: ubuntu-latest

From 64c138101654908bf3b02a20efc6f7397165fb4a Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 20 Sep 2024 09:06:57 +0200
Subject: [PATCH 08/21] Add github workflow gendercheck test and lint

---
 .github/workflows/gendercheck_lint.yml | 11 +++++
 .github/workflows/gendercheck_test.yml | 60 ++++++++++++++++++++++++++
 2 files changed, 71 insertions(+)
 create mode 100644 .github/workflows/gendercheck_lint.yml
 create mode 100644 .github/workflows/gendercheck_test.yml

diff --git a/.github/workflows/gendercheck_lint.yml b/.github/workflows/gendercheck_lint.yml
new file mode 100644
index 0000000..b1c7d3b
--- /dev/null
+++ b/.github/workflows/gendercheck_lint.yml
@@ -0,0 +1,11 @@
+name: GenderCheck Lint
+on:
+  pull_request:
+    paths: GenderCheck/**
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/gendercheck_test.yml b/.github/workflows/gendercheck_test.yml
new file mode 100644
index 0000000..374644f
--- /dev/null
+++ b/.github/workflows/gendercheck_test.yml
@@ -0,0 +1,60 @@
+# Source: https://github.com/marketplace/actions/install-poetry-action
+name: GenderCheck Test
+on:
+  pull_request:
+    paths: GenderCheck/**
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: GenderCheck/
+    steps:
+      #----------------------------------------------
+      # check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up python
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11.5'
+      #----------------------------------------------
+      # install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      #----------------------------------------------
+      # load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: venv_gendercheck-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+      #----------------------------------------------
+      # install root project
+      #----------------------------------------------
+      - name: Install project
+        run: poetry install --no-interaction
+      #----------------------------------------------
+      # run pytest
+      #----------------------------------------------
+      - name: Run tests
+        run: |
+          source .venv/bin/activate
+          pytest .

From 6b836e8dbcfa623d64a6b099b17cbb59dabc9c32 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 20 Sep 2024 09:42:16 +0200
Subject: [PATCH 09/21] add pyproject.toml and poetry.lock

---
 GenderCheck/poetry.lock    | 124 +++++++++++++++++++++++++++++++++++++
 GenderCheck/pyproject.toml |  24 +++++++
 2 files changed, 148 insertions(+)
 create mode 100644 GenderCheck/poetry.lock
 create mode 100644 GenderCheck/pyproject.toml

diff --git a/GenderCheck/poetry.lock b/GenderCheck/poetry.lock
new file mode 100644
index 0000000..35868e0
--- /dev/null
+++ b/GenderCheck/poetry.lock
@@ -0,0 +1,124 @@
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+description = "Cross-platform colored terminal text."
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
+]
+
+[[package]]
+name = "iniconfig"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
+
+[[package]]
+name = "packaging"
+version = "23.2"
+description = "Core utilities for Python packages"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
+    {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
+]
+
+[[package]]
+name = "pluggy"
+version = "1.4.0"
+description = "plugin and hook calling mechanisms for python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pluggy-1.4.0-py3-none-any.whl", hash = "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"},
+    {file = "pluggy-1.4.0.tar.gz", hash = "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"},
+]
+
+[package.extras]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
+
+[[package]]
+name = "pysam"
+version = "0.22.0"
+description = "Package for reading, manipulating, and writing genomic data"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "pysam-0.22.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:116278a7caa122b2b8acc56d13b3599be9b1236f27a12488bffc306858ff0d57"},
+    {file = "pysam-0.22.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:da2f1af461e44d5c2c7210d458ee216f8ab98486adf1eea6c88eea5c1058a62f"},
+    {file = "pysam-0.22.0-cp310-cp310-manylinux_2_28_aarch64.whl", hash = "sha256:021fbf6874ad998aba19be33828ad9d23d52273643793488ac4b12917d714c68"},
+    {file = "pysam-0.22.0-cp310-cp310-manylinux_2_28_x86_64.whl", hash = "sha256:26199e403855b9da45341d25682e0df27013687d9cb1b4fd328136fbd506292b"},
+    {file = "pysam-0.22.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:9bfebf89b1dc2ff6f88d64b5f05d8630deb89562b22764f8ee7f6fa9e677bb91"},
+    {file = "pysam-0.22.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:942dd4a2263996bc2daa21200886e9fde027f32ce8820e7832b20bbdb97eb393"},
+    {file = "pysam-0.22.0-cp311-cp311-manylinux_2_28_aarch64.whl", hash = "sha256:83776ba587eb9575a209efed1cedb49d69c5fa6cc520dd722a0a09d0bb4e9b87"},
+    {file = "pysam-0.22.0-cp311-cp311-manylinux_2_28_x86_64.whl", hash = "sha256:4779a99d1ece17a98724d87a5c10c455cf212b3baa3a8399d3d072e4d0ae5ba0"},
+    {file = "pysam-0.22.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:bb61bf30c15f6767403b423b04c293e96fd7635457b506c849aafcf48fc13242"},
+    {file = "pysam-0.22.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:32042e0bf3c5dd8554769442c2e1f7b6ada902c33ee44c616d0403e7acd12ee3"},
+    {file = "pysam-0.22.0-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:f23b2f47528b94e8abe3b700103fb1214c623ae1c1b8125ecf22d4d33d76720f"},
+    {file = "pysam-0.22.0-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:cfd2b858c7405cf38c730cba779ddf9f8cff28b4842c6440e64781650dcb9a52"},
+    {file = "pysam-0.22.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:87dbf72f3e61fd6d3f92b1b683d9a9e797b6cc213ffcd971899f24a16f9f6e8f"},
+    {file = "pysam-0.22.0-cp36-cp36m-manylinux_2_28_aarch64.whl", hash = "sha256:9af1cd3d07fd4c84e9b3d8a46c65b25f95278185bc6d44c4a48951679d5189ac"},
+    {file = "pysam-0.22.0-cp36-cp36m-manylinux_2_28_x86_64.whl", hash = "sha256:f73d7923c89618fb7024875ed8eddc5fb0c911f430e3495de482fcee48143e45"},
+    {file = "pysam-0.22.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:6ffe5c98725fea54b1b2aa8f14a60ee9ceaed32c04460d1b861a62603dcd7153"},
+    {file = "pysam-0.22.0-cp37-cp37m-manylinux_2_28_aarch64.whl", hash = "sha256:34f5653a82138d28a8e86205785a0398eb6c89f776b4145ff42783168757323c"},
+    {file = "pysam-0.22.0-cp37-cp37m-manylinux_2_28_x86_64.whl", hash = "sha256:9d3ebb1515c2fd9b11823469e5b211ca3cc89e976c00c284a2190804c9f11726"},
+    {file = "pysam-0.22.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:9b8e18520e7a79bad91b44cf9199c7fa42cec5c3020024d7ef9a7161d0099bf8"},
+    {file = "pysam-0.22.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a98d1ddca64943f3ead507721e52466aea2f7303e549d4960a2eb1d9fff8e3d7"},
+    {file = "pysam-0.22.0-cp38-cp38-manylinux_2_28_aarch64.whl", hash = "sha256:6d6aa2346b11ad35e88c65eb0067321318c25c7f35f75c98061173eabefcf8b0"},
+    {file = "pysam-0.22.0-cp38-cp38-manylinux_2_28_x86_64.whl", hash = "sha256:4f6657a09c81333adb5545cf9a20d4c2ca1686acf8609ad58f13b3ec1b52a9cf"},
+    {file = "pysam-0.22.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:93eb12be3822fb387e5438811f62a0f5e56c1edd5c830aaa316fb50d3d0bc181"},
+    {file = "pysam-0.22.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:9ba53f9b0b2c5cb57908855cdb35a31b34c5211d215aa01bdb3e9b3d05c659cc"},
+    {file = "pysam-0.22.0-cp39-cp39-manylinux_2_28_aarch64.whl", hash = "sha256:1b84f99aa04e30bd1cc35c01bd41c2b7680131f56c71a740805aff8086f24b56"},
+    {file = "pysam-0.22.0-cp39-cp39-manylinux_2_28_x86_64.whl", hash = "sha256:481e4efbfbc07b6b92194a005cb9a98006c8378024f41c7b66c58b14f6e77f9c"},
+    {file = "pysam-0.22.0.tar.gz", hash = "sha256:ab7a46973cf0ab8c6ac327f4c3fb67698d7ccbeef8631a716898c6ba01ef3e45"},
+]
+
+[[package]]
+name = "pytest"
+version = "8.0.2"
+description = "pytest: simple powerful testing with Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pytest-8.0.2-py3-none-any.whl", hash = "sha256:edfaaef32ce5172d5466b5127b42e0d6d35ebbe4453f0e3505d96afd93f6b096"},
+    {file = "pytest-8.0.2.tar.gz", hash = "sha256:d4051d623a2e0b7e51960ba963193b09ce6daeb9759a451844a21e4ddedfc1bd"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=1.3.0,<2.0"
+
+[package.extras]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+
+[[package]]
+name = "pytest-datadir"
+version = "1.5.0"
+description = "pytest plugin for test data directories and files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pytest-datadir-1.5.0.tar.gz", hash = "sha256:1617ed92f9afda0c877e4eac91904b5f779d24ba8f5e438752e3ae39d8d2ee3f"},
+    {file = "pytest_datadir-1.5.0-py3-none-any.whl", hash = "sha256:34adf361bcc7b37961bbc1dfa8d25a4829e778bab461703c38a5c50ca9c36dc8"},
+]
+
+[package.dependencies]
+pytest = ">=5.0"
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.11"
+content-hash = "f25c942350acba89051a081c7b7a93c1d8ba2e970ee295290d94a6e7b9285398"
diff --git a/GenderCheck/pyproject.toml b/GenderCheck/pyproject.toml
new file mode 100644
index 0000000..0ef8d2f
--- /dev/null
+++ b/GenderCheck/pyproject.toml
@@ -0,0 +1,24 @@
+[tool.poetry]
+name = "gendercheck"
+version = "0.1.0"
+description = ""
+authors = ["Your Name <you@example.com>"]
+license = "MIT"
+package-mode = false
+
+[tool.poetry.dependencies]
+python = "^3.11"
+iniconfig = "2.0.0"
+packaging = "23.2"
+pluggy = "1.4.0"
+pysam = "0.22.0"
+pytest = "8.0.2"
+pytest-datadir = "^1.5.0"
+
+[tool.ruff]
+line-length = 127
+indent-width = 4
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

From b412262c2c6292d97eff4d1d2b9d328750da90d8 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 20 Sep 2024 09:46:48 +0200
Subject: [PATCH 10/21] Add mosaichunter github actions workflow

---
 .github/workflows/moisaichunter_lint.yml |  11 ++
 .github/workflows/moisaichunter_test.yml |  60 +++++++++++
 MosaicHunter/1.0.0/poetry.lock           | 124 +++++++++++++++++++++++
 MosaicHunter/1.0.0/pyproject.toml        |  24 +++++
 4 files changed, 219 insertions(+)
 create mode 100644 .github/workflows/moisaichunter_lint.yml
 create mode 100644 .github/workflows/moisaichunter_test.yml
 create mode 100644 MosaicHunter/1.0.0/poetry.lock
 create mode 100644 MosaicHunter/1.0.0/pyproject.toml

diff --git a/.github/workflows/moisaichunter_lint.yml b/.github/workflows/moisaichunter_lint.yml
new file mode 100644
index 0000000..f12ea7d
--- /dev/null
+++ b/.github/workflows/moisaichunter_lint.yml
@@ -0,0 +1,11 @@
+name: MosaicHunter Lint
+on:
+  pull_request:
+    paths: MosaicHunter/**
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/moisaichunter_test.yml b/.github/workflows/moisaichunter_test.yml
new file mode 100644
index 0000000..d94fd59
--- /dev/null
+++ b/.github/workflows/moisaichunter_test.yml
@@ -0,0 +1,60 @@
+# Source: https://github.com/marketplace/actions/install-poetry-action
+name: MosaicHunter Test
+on:
+  pull_request:
+    paths: MosaicHunter/**
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: MosaicHunter/1.0.0/
+    steps:
+      #----------------------------------------------
+      # check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up python
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11.5'
+      #----------------------------------------------
+      # install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      #----------------------------------------------
+      # load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: venv_mosaichunter-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+      #----------------------------------------------
+      # install root project
+      #----------------------------------------------
+      - name: Install project
+        run: poetry install --no-interaction
+      #----------------------------------------------
+      # run pytest
+      #----------------------------------------------
+      - name: Run tests
+        run: |
+          source .venv/bin/activate
+          pytest .
diff --git a/MosaicHunter/1.0.0/poetry.lock b/MosaicHunter/1.0.0/poetry.lock
new file mode 100644
index 0000000..35868e0
--- /dev/null
+++ b/MosaicHunter/1.0.0/poetry.lock
@@ -0,0 +1,124 @@
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+description = "Cross-platform colored terminal text."
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
+]
+
+[[package]]
+name = "iniconfig"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
+
+[[package]]
+name = "packaging"
+version = "23.2"
+description = "Core utilities for Python packages"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
+    {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
+]
+
+[[package]]
+name = "pluggy"
+version = "1.4.0"
+description = "plugin and hook calling mechanisms for python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pluggy-1.4.0-py3-none-any.whl", hash = "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"},
+    {file = "pluggy-1.4.0.tar.gz", hash = "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"},
+]
+
+[package.extras]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
+
+[[package]]
+name = "pysam"
+version = "0.22.0"
+description = "Package for reading, manipulating, and writing genomic data"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "pysam-0.22.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:116278a7caa122b2b8acc56d13b3599be9b1236f27a12488bffc306858ff0d57"},
+    {file = "pysam-0.22.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:da2f1af461e44d5c2c7210d458ee216f8ab98486adf1eea6c88eea5c1058a62f"},
+    {file = "pysam-0.22.0-cp310-cp310-manylinux_2_28_aarch64.whl", hash = "sha256:021fbf6874ad998aba19be33828ad9d23d52273643793488ac4b12917d714c68"},
+    {file = "pysam-0.22.0-cp310-cp310-manylinux_2_28_x86_64.whl", hash = "sha256:26199e403855b9da45341d25682e0df27013687d9cb1b4fd328136fbd506292b"},
+    {file = "pysam-0.22.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:9bfebf89b1dc2ff6f88d64b5f05d8630deb89562b22764f8ee7f6fa9e677bb91"},
+    {file = "pysam-0.22.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:942dd4a2263996bc2daa21200886e9fde027f32ce8820e7832b20bbdb97eb393"},
+    {file = "pysam-0.22.0-cp311-cp311-manylinux_2_28_aarch64.whl", hash = "sha256:83776ba587eb9575a209efed1cedb49d69c5fa6cc520dd722a0a09d0bb4e9b87"},
+    {file = "pysam-0.22.0-cp311-cp311-manylinux_2_28_x86_64.whl", hash = "sha256:4779a99d1ece17a98724d87a5c10c455cf212b3baa3a8399d3d072e4d0ae5ba0"},
+    {file = "pysam-0.22.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:bb61bf30c15f6767403b423b04c293e96fd7635457b506c849aafcf48fc13242"},
+    {file = "pysam-0.22.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:32042e0bf3c5dd8554769442c2e1f7b6ada902c33ee44c616d0403e7acd12ee3"},
+    {file = "pysam-0.22.0-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:f23b2f47528b94e8abe3b700103fb1214c623ae1c1b8125ecf22d4d33d76720f"},
+    {file = "pysam-0.22.0-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:cfd2b858c7405cf38c730cba779ddf9f8cff28b4842c6440e64781650dcb9a52"},
+    {file = "pysam-0.22.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:87dbf72f3e61fd6d3f92b1b683d9a9e797b6cc213ffcd971899f24a16f9f6e8f"},
+    {file = "pysam-0.22.0-cp36-cp36m-manylinux_2_28_aarch64.whl", hash = "sha256:9af1cd3d07fd4c84e9b3d8a46c65b25f95278185bc6d44c4a48951679d5189ac"},
+    {file = "pysam-0.22.0-cp36-cp36m-manylinux_2_28_x86_64.whl", hash = "sha256:f73d7923c89618fb7024875ed8eddc5fb0c911f430e3495de482fcee48143e45"},
+    {file = "pysam-0.22.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:6ffe5c98725fea54b1b2aa8f14a60ee9ceaed32c04460d1b861a62603dcd7153"},
+    {file = "pysam-0.22.0-cp37-cp37m-manylinux_2_28_aarch64.whl", hash = "sha256:34f5653a82138d28a8e86205785a0398eb6c89f776b4145ff42783168757323c"},
+    {file = "pysam-0.22.0-cp37-cp37m-manylinux_2_28_x86_64.whl", hash = "sha256:9d3ebb1515c2fd9b11823469e5b211ca3cc89e976c00c284a2190804c9f11726"},
+    {file = "pysam-0.22.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:9b8e18520e7a79bad91b44cf9199c7fa42cec5c3020024d7ef9a7161d0099bf8"},
+    {file = "pysam-0.22.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a98d1ddca64943f3ead507721e52466aea2f7303e549d4960a2eb1d9fff8e3d7"},
+    {file = "pysam-0.22.0-cp38-cp38-manylinux_2_28_aarch64.whl", hash = "sha256:6d6aa2346b11ad35e88c65eb0067321318c25c7f35f75c98061173eabefcf8b0"},
+    {file = "pysam-0.22.0-cp38-cp38-manylinux_2_28_x86_64.whl", hash = "sha256:4f6657a09c81333adb5545cf9a20d4c2ca1686acf8609ad58f13b3ec1b52a9cf"},
+    {file = "pysam-0.22.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:93eb12be3822fb387e5438811f62a0f5e56c1edd5c830aaa316fb50d3d0bc181"},
+    {file = "pysam-0.22.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:9ba53f9b0b2c5cb57908855cdb35a31b34c5211d215aa01bdb3e9b3d05c659cc"},
+    {file = "pysam-0.22.0-cp39-cp39-manylinux_2_28_aarch64.whl", hash = "sha256:1b84f99aa04e30bd1cc35c01bd41c2b7680131f56c71a740805aff8086f24b56"},
+    {file = "pysam-0.22.0-cp39-cp39-manylinux_2_28_x86_64.whl", hash = "sha256:481e4efbfbc07b6b92194a005cb9a98006c8378024f41c7b66c58b14f6e77f9c"},
+    {file = "pysam-0.22.0.tar.gz", hash = "sha256:ab7a46973cf0ab8c6ac327f4c3fb67698d7ccbeef8631a716898c6ba01ef3e45"},
+]
+
+[[package]]
+name = "pytest"
+version = "8.0.2"
+description = "pytest: simple powerful testing with Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pytest-8.0.2-py3-none-any.whl", hash = "sha256:edfaaef32ce5172d5466b5127b42e0d6d35ebbe4453f0e3505d96afd93f6b096"},
+    {file = "pytest-8.0.2.tar.gz", hash = "sha256:d4051d623a2e0b7e51960ba963193b09ce6daeb9759a451844a21e4ddedfc1bd"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=1.3.0,<2.0"
+
+[package.extras]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+
+[[package]]
+name = "pytest-datadir"
+version = "1.5.0"
+description = "pytest plugin for test data directories and files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pytest-datadir-1.5.0.tar.gz", hash = "sha256:1617ed92f9afda0c877e4eac91904b5f779d24ba8f5e438752e3ae39d8d2ee3f"},
+    {file = "pytest_datadir-1.5.0-py3-none-any.whl", hash = "sha256:34adf361bcc7b37961bbc1dfa8d25a4829e778bab461703c38a5c50ca9c36dc8"},
+]
+
+[package.dependencies]
+pytest = ">=5.0"
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.11"
+content-hash = "f25c942350acba89051a081c7b7a93c1d8ba2e970ee295290d94a6e7b9285398"
diff --git a/MosaicHunter/1.0.0/pyproject.toml b/MosaicHunter/1.0.0/pyproject.toml
new file mode 100644
index 0000000..7cda6f9
--- /dev/null
+++ b/MosaicHunter/1.0.0/pyproject.toml
@@ -0,0 +1,24 @@
+[tool.poetry]
+name = "mosaichunter"
+version = "1.0.0"
+description = ""
+authors = ["Your Name <you@example.com>"]
+license = "MIT"
+package-mode = false
+
+[tool.poetry.dependencies]
+python = "^3.11"
+iniconfig = "2.0.0"
+packaging = "23.2"
+pluggy = "1.4.0"
+pysam = "0.22.0"
+pytest = "8.0.2"
+pytest-datadir = "^1.5.0"
+
+[tool.ruff]
+line-length = 127
+indent-width = 4
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

From 496bf9fe9caad3a7ac3b4d76e5393ca16ef2d961 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 27 Sep 2024 10:50:34 +0200
Subject: [PATCH 11/21] github workflows add on push

---
 .github/workflows/checkqc_lint.yml       | 2 ++
 .github/workflows/checkqc_test.yml       | 2 ++
 .github/workflows/gendercheck_lint.yml   | 2 ++
 .github/workflows/moisaichunter_lint.yml | 2 ++
 .github/workflows/moisaichunter_test.yml | 2 ++
 5 files changed, 10 insertions(+)

diff --git a/.github/workflows/checkqc_lint.yml b/.github/workflows/checkqc_lint.yml
index 94d80dc..95ed78a 100644
--- a/.github/workflows/checkqc_lint.yml
+++ b/.github/workflows/checkqc_lint.yml
@@ -2,6 +2,8 @@ name: CheckQC Lint
 on:
   pull_request:
     paths: CheckQC/**
+  push:
+    branches: [master, develop]
 
 jobs:
   ruff:
diff --git a/.github/workflows/checkqc_test.yml b/.github/workflows/checkqc_test.yml
index 6e48cc6..928029b 100644
--- a/.github/workflows/checkqc_test.yml
+++ b/.github/workflows/checkqc_test.yml
@@ -3,6 +3,8 @@ name: CheckQC Test
 on:
   pull_request:
     paths: CheckQC/**
+  push:
+    branches: [master, develop]
 
 jobs:
   pytest:
diff --git a/.github/workflows/gendercheck_lint.yml b/.github/workflows/gendercheck_lint.yml
index b1c7d3b..6beaabf 100644
--- a/.github/workflows/gendercheck_lint.yml
+++ b/.github/workflows/gendercheck_lint.yml
@@ -2,6 +2,8 @@ name: GenderCheck Lint
 on:
   pull_request:
     paths: GenderCheck/**
+  push:
+    branches: [master, develop]
 
 jobs:
   ruff:
diff --git a/.github/workflows/moisaichunter_lint.yml b/.github/workflows/moisaichunter_lint.yml
index f12ea7d..3a014ad 100644
--- a/.github/workflows/moisaichunter_lint.yml
+++ b/.github/workflows/moisaichunter_lint.yml
@@ -2,6 +2,8 @@ name: MosaicHunter Lint
 on:
   pull_request:
     paths: MosaicHunter/**
+  push:
+    branches: [master, develop]
 
 jobs:
   ruff:
diff --git a/.github/workflows/moisaichunter_test.yml b/.github/workflows/moisaichunter_test.yml
index d94fd59..00f2548 100644
--- a/.github/workflows/moisaichunter_test.yml
+++ b/.github/workflows/moisaichunter_test.yml
@@ -3,6 +3,8 @@ name: MosaicHunter Test
 on:
   pull_request:
     paths: MosaicHunter/**
+  push:
+    branches: [master, develop]
 
 jobs:
   pytest:

From 4c678bba1828b54dcd37dcf62e8f1b9e96bbd989 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 27 Sep 2024 11:12:21 +0200
Subject: [PATCH 12/21] Add poetry group dev dependencies and update
 conflicting package pluggy

---
 CheckQC/poetry.lock               |  8 ++++----
 CheckQC/pyproject.toml            |  1 -
 GenderCheck/poetry.lock           | 18 +++++++++---------
 GenderCheck/pyproject.toml        |  6 ++++--
 MosaicHunter/1.0.0/poetry.lock    |  8 ++++----
 MosaicHunter/1.0.0/pyproject.toml |  4 +++-
 6 files changed, 24 insertions(+), 21 deletions(-)

diff --git a/CheckQC/poetry.lock b/CheckQC/poetry.lock
index 8b10920..02c3676 100644
--- a/CheckQC/poetry.lock
+++ b/CheckQC/poetry.lock
@@ -616,16 +616,16 @@ files = [
 
 [[package]]
 name = "tzdata"
-version = "2024.1"
+version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
-    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
+    {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"},
+    {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"},
 ]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11.4"
-content-hash = "b9545131c195e37f949ffff6f6a065464f501b7922094a291b51a93cfc521886"
+content-hash = "77b250569def1ef2cca5b0540b0860096cf89b8a35737341f75c9a00f3162b9f"
diff --git a/CheckQC/pyproject.toml b/CheckQC/pyproject.toml
index c7e7591..ea711c4 100644
--- a/CheckQC/pyproject.toml
+++ b/CheckQC/pyproject.toml
@@ -10,7 +10,6 @@ package-mode = false
 python = "^3.11.4"
 pandas = "2.1.4"
 pyyaml = "6.0.1"
-pytest = "^8.3.3"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.3.3"
diff --git a/GenderCheck/poetry.lock b/GenderCheck/poetry.lock
index 35868e0..7220270 100644
--- a/GenderCheck/poetry.lock
+++ b/GenderCheck/poetry.lock
@@ -35,13 +35,13 @@ files = [
 
 [[package]]
 name = "pluggy"
-version = "1.4.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pluggy-1.4.0-py3-none-any.whl", hash = "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"},
-    {file = "pluggy-1.4.0.tar.gz", hash = "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"},
+    {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"},
+    {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"},
 ]
 
 [package.extras]
@@ -86,23 +86,23 @@ files = [
 
 [[package]]
 name = "pytest"
-version = "8.0.2"
+version = "8.3.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pytest-8.0.2-py3-none-any.whl", hash = "sha256:edfaaef32ce5172d5466b5127b42e0d6d35ebbe4453f0e3505d96afd93f6b096"},
-    {file = "pytest-8.0.2.tar.gz", hash = "sha256:d4051d623a2e0b7e51960ba963193b09ce6daeb9759a451844a21e4ddedfc1bd"},
+    {file = "pytest-8.3.3-py3-none-any.whl", hash = "sha256:a6853c7375b2663155079443d2e45de913a911a11d669df02a50814944db57b2"},
+    {file = "pytest-8.3.3.tar.gz", hash = "sha256:70b98107bd648308a7952b06e6ca9a50bc660be218d53c257cc1fc94fda10181"},
 ]
 
 [package.dependencies]
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=1.3.0,<2.0"
+pluggy = ">=1.5,<2"
 
 [package.extras]
-testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-datadir"
@@ -121,4 +121,4 @@ pytest = ">=5.0"
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "f25c942350acba89051a081c7b7a93c1d8ba2e970ee295290d94a6e7b9285398"
+content-hash = "9d44fccb4bb8753f5ac3dff1ee21c05e4475867600ce65d0c6809bc7d3628302"
diff --git a/GenderCheck/pyproject.toml b/GenderCheck/pyproject.toml
index 0ef8d2f..3c87838 100644
--- a/GenderCheck/pyproject.toml
+++ b/GenderCheck/pyproject.toml
@@ -10,9 +10,11 @@ package-mode = false
 python = "^3.11"
 iniconfig = "2.0.0"
 packaging = "23.2"
-pluggy = "1.4.0"
+pluggy = "^1.5.0"
 pysam = "0.22.0"
-pytest = "8.0.2"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.3.3"
 pytest-datadir = "^1.5.0"
 
 [tool.ruff]
diff --git a/MosaicHunter/1.0.0/poetry.lock b/MosaicHunter/1.0.0/poetry.lock
index 35868e0..cfb23f6 100644
--- a/MosaicHunter/1.0.0/poetry.lock
+++ b/MosaicHunter/1.0.0/poetry.lock
@@ -35,13 +35,13 @@ files = [
 
 [[package]]
 name = "pluggy"
-version = "1.4.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pluggy-1.4.0-py3-none-any.whl", hash = "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"},
-    {file = "pluggy-1.4.0.tar.gz", hash = "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"},
+    {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"},
+    {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"},
 ]
 
 [package.extras]
@@ -121,4 +121,4 @@ pytest = ">=5.0"
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "f25c942350acba89051a081c7b7a93c1d8ba2e970ee295290d94a6e7b9285398"
+content-hash = "d2dc5a03871e9ede54e5fc47a1cb8cc3f1adefd93e3f4b354b4871cbdc60e08d"
diff --git a/MosaicHunter/1.0.0/pyproject.toml b/MosaicHunter/1.0.0/pyproject.toml
index 7cda6f9..f98b9a7 100644
--- a/MosaicHunter/1.0.0/pyproject.toml
+++ b/MosaicHunter/1.0.0/pyproject.toml
@@ -10,8 +10,10 @@ package-mode = false
 python = "^3.11"
 iniconfig = "2.0.0"
 packaging = "23.2"
-pluggy = "1.4.0"
+pluggy = "1.5.0"
 pysam = "0.22.0"
+
+[tool.poetry.group.dev.dependencies]
 pytest = "8.0.2"
 pytest-datadir = "^1.5.0"
 

From 1705db193a5717c7e7727b8eb76b22cfd23030e8 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 27 Sep 2024 11:16:26 +0200
Subject: [PATCH 13/21] add working dir ruff

---
 .github/workflows/checkqc_lint.yml       | 3 +++
 .github/workflows/gendercheck_lint.yml   | 3 +++
 .github/workflows/moisaichunter_lint.yml | 3 +++
 3 files changed, 9 insertions(+)

diff --git a/.github/workflows/checkqc_lint.yml b/.github/workflows/checkqc_lint.yml
index 95ed78a..3391620 100644
--- a/.github/workflows/checkqc_lint.yml
+++ b/.github/workflows/checkqc_lint.yml
@@ -8,6 +8,9 @@ on:
 jobs:
   ruff:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: CheckQC/
     steps:
       - uses: actions/checkout@v4
       - uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/gendercheck_lint.yml b/.github/workflows/gendercheck_lint.yml
index 6beaabf..7586f84 100644
--- a/.github/workflows/gendercheck_lint.yml
+++ b/.github/workflows/gendercheck_lint.yml
@@ -8,6 +8,9 @@ on:
 jobs:
   ruff:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: GenderCheck/
     steps:
       - uses: actions/checkout@v4
       - uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/moisaichunter_lint.yml b/.github/workflows/moisaichunter_lint.yml
index 3a014ad..fb6c0f9 100644
--- a/.github/workflows/moisaichunter_lint.yml
+++ b/.github/workflows/moisaichunter_lint.yml
@@ -8,6 +8,9 @@ on:
 jobs:
   ruff:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: MosaicHunter/1.0.0//
     steps:
       - uses: actions/checkout@v4
       - uses: chartboost/ruff-action@v1

From cef72724f2cdcc3c619576c7f1fa86444dd84b32 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 27 Sep 2024 11:17:19 +0200
Subject: [PATCH 14/21] fix incorrect type to array in filter paths

---
 .github/workflows/checkqc_lint.yml       | 2 +-
 .github/workflows/checkqc_test.yml       | 2 +-
 .github/workflows/gendercheck_lint.yml   | 2 +-
 .github/workflows/gendercheck_test.yml   | 3 ++-
 .github/workflows/moisaichunter_lint.yml | 2 +-
 .github/workflows/moisaichunter_test.yml | 2 +-
 6 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/checkqc_lint.yml b/.github/workflows/checkqc_lint.yml
index 3391620..fcd49e9 100644
--- a/.github/workflows/checkqc_lint.yml
+++ b/.github/workflows/checkqc_lint.yml
@@ -1,7 +1,7 @@
 name: CheckQC Lint
 on:
   pull_request:
-    paths: CheckQC/**
+    paths: [CheckQC/**]
   push:
     branches: [master, develop]
 
diff --git a/.github/workflows/checkqc_test.yml b/.github/workflows/checkqc_test.yml
index 928029b..2ab9133 100644
--- a/.github/workflows/checkqc_test.yml
+++ b/.github/workflows/checkqc_test.yml
@@ -2,7 +2,7 @@
 name: CheckQC Test
 on:
   pull_request:
-    paths: CheckQC/**
+    paths: [CheckQC/**]
   push:
     branches: [master, develop]
 
diff --git a/.github/workflows/gendercheck_lint.yml b/.github/workflows/gendercheck_lint.yml
index 7586f84..cece608 100644
--- a/.github/workflows/gendercheck_lint.yml
+++ b/.github/workflows/gendercheck_lint.yml
@@ -1,7 +1,7 @@
 name: GenderCheck Lint
 on:
   pull_request:
-    paths: GenderCheck/**
+    paths: [GenderCheck/**]
   push:
     branches: [master, develop]
 
diff --git a/.github/workflows/gendercheck_test.yml b/.github/workflows/gendercheck_test.yml
index 374644f..4f3c700 100644
--- a/.github/workflows/gendercheck_test.yml
+++ b/.github/workflows/gendercheck_test.yml
@@ -2,7 +2,8 @@
 name: GenderCheck Test
 on:
   pull_request:
-    paths: GenderCheck/**
+    paths: [GenderCheck/**]
+  push:
 
 jobs:
   pytest:
diff --git a/.github/workflows/moisaichunter_lint.yml b/.github/workflows/moisaichunter_lint.yml
index fb6c0f9..5742c9d 100644
--- a/.github/workflows/moisaichunter_lint.yml
+++ b/.github/workflows/moisaichunter_lint.yml
@@ -1,7 +1,7 @@
 name: MosaicHunter Lint
 on:
   pull_request:
-    paths: MosaicHunter/**
+    paths: [MosaicHunter/**]
   push:
     branches: [master, develop]
 
diff --git a/.github/workflows/moisaichunter_test.yml b/.github/workflows/moisaichunter_test.yml
index 00f2548..c88aab0 100644
--- a/.github/workflows/moisaichunter_test.yml
+++ b/.github/workflows/moisaichunter_test.yml
@@ -2,7 +2,7 @@
 name: MosaicHunter Test
 on:
   pull_request:
-    paths: MosaicHunter/**
+    paths: [MosaicHunter/**]
   push:
     branches: [master, develop]
 

From 56162853a72aab2a02fe91831587b0ac4be22c9f Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 27 Sep 2024 11:17:29 +0200
Subject: [PATCH 15/21] add on push

---
 .github/workflows/gendercheck_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/gendercheck_test.yml b/.github/workflows/gendercheck_test.yml
index 4f3c700..f92821a 100644
--- a/.github/workflows/gendercheck_test.yml
+++ b/.github/workflows/gendercheck_test.yml
@@ -4,6 +4,7 @@ on:
   pull_request:
     paths: [GenderCheck/**]
   push:
+    branches: [master, develop]
 
 jobs:
   pytest:

From 32b0a232fd942e48e6efe9c03208b81ec42151e6 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 27 Sep 2024 11:17:43 +0200
Subject: [PATCH 16/21] fix regex string

---
 Utils/create_hsmetrics_summary.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Utils/create_hsmetrics_summary.py b/Utils/create_hsmetrics_summary.py
index 4256fc3..582b61e 100644
--- a/Utils/create_hsmetrics_summary.py
+++ b/Utils/create_hsmetrics_summary.py
@@ -8,7 +8,7 @@
     parser.add_argument('hsmetrics_files', type=argparse.FileType('r'), nargs='*', help='HSMetric file')
     arguments = parser.parse_args()
 
-    interval_files_pattern = re.compile("BAIT_INTERVALS=\[(\S*)\].TARGET_INTERVALS=\[(\S*)\]")  # noqa: W605
+    interval_files_pattern = re.compile(r"BAIT_INTERVALS=\[(\S*)\].TARGET_INTERVALS=\[(\S*)\]")
     summary_header = []
     summary_data = {}
     for hsmetrics_file in arguments.hsmetrics_files:

From 27b913146d9d162402f7e61725c4e14f2075fbba Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 27 Sep 2024 11:46:19 +0200
Subject: [PATCH 17/21] add pre-commit ruff

---
 .pre-commit-config.yaml |  11 +++
 poetry.lock             | 181 +++++++++++++++++++++++++++++++++++++++-
 pyproject.toml          |   3 +
 3 files changed, 194 insertions(+), 1 deletion(-)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..8f4b8b5
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,11 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      # Ruff version.
+      rev: v0.5.1
+      hooks:
+          # Run the linter.
+          - id: ruff
+          # Run the formatter.
+          - id: ruff-format
diff --git a/poetry.lock b/poetry.lock
index d886a2b..0e00519 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,16 @@
 # This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
+[[package]]
+name = "cfgv"
+version = "3.4.0"
+description = "Validate configuration and produce human readable error messages."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
+    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
+]
+
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -11,6 +22,47 @@ files = [
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
+[[package]]
+name = "distlib"
+version = "0.3.8"
+description = "Distribution utilities"
+optional = false
+python-versions = "*"
+files = [
+    {file = "distlib-0.3.8-py2.py3-none-any.whl", hash = "sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784"},
+    {file = "distlib-0.3.8.tar.gz", hash = "sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64"},
+]
+
+[[package]]
+name = "filelock"
+version = "3.16.1"
+description = "A platform independent file lock."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "filelock-3.16.1-py3-none-any.whl", hash = "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0"},
+    {file = "filelock-3.16.1.tar.gz", hash = "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435"},
+]
+
+[package.extras]
+docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4.1)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"]
+typing = ["typing-extensions (>=4.12.2)"]
+
+[[package]]
+name = "identify"
+version = "2.6.1"
+description = "File identification library for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "identify-2.6.1-py2.py3-none-any.whl", hash = "sha256:53863bcac7caf8d2ed85bd20312ea5dcfc22226800f6d6881f232d861db5a8f0"},
+    {file = "identify-2.6.1.tar.gz", hash = "sha256:91478c5fb7c3aac5ff7bf9b4344f803843dc586832d5f110d672b19aa1984c98"},
+]
+
+[package.extras]
+license = ["ukkonen"]
+
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
@@ -22,6 +74,17 @@ files = [
     {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
 ]
 
+[[package]]
+name = "nodeenv"
+version = "1.9.1"
+description = "Node.js virtual environment builder"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
+    {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"},
+    {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"},
+]
+
 [[package]]
 name = "packaging"
 version = "24.1"
@@ -33,6 +96,22 @@ files = [
     {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
 ]
 
+[[package]]
+name = "platformdirs"
+version = "4.3.6"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "platformdirs-4.3.6-py3-none-any.whl", hash = "sha256:73e575e1408ab8103900836b97580d5307456908a03e92031bab39e4554cc3fb"},
+    {file = "platformdirs-4.3.6.tar.gz", hash = "sha256:357fb2acbc885b0419afd3ce3ed34564c13c9b95c89360cd9563f73aa5e2b907"},
+]
+
+[package.extras]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
+
 [[package]]
 name = "pluggy"
 version = "1.5.0"
@@ -48,6 +127,24 @@ files = [
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
+[[package]]
+name = "pre-commit"
+version = "3.8.0"
+description = "A framework for managing and maintaining multi-language pre-commit hooks."
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "pre_commit-3.8.0-py2.py3-none-any.whl", hash = "sha256:9a90a53bf82fdd8778d58085faf8d83df56e40dfe18f45b19446e26bf1b3a63f"},
+    {file = "pre_commit-3.8.0.tar.gz", hash = "sha256:8bb6494d4a20423842e198980c9ecf9f96607a07ea29549e180eef9ae80fe7af"},
+]
+
+[package.dependencies]
+cfgv = ">=2.0.0"
+identify = ">=1.0.0"
+nodeenv = ">=0.11.1"
+pyyaml = ">=5.1"
+virtualenv = ">=20.10.0"
+
 [[package]]
 name = "pytest"
 version = "8.3.3"
@@ -68,7 +165,89 @@ pluggy = ">=1.5,<2"
 [package.extras]
 dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
+[[package]]
+name = "pyyaml"
+version = "6.0.2"
+description = "YAML parser and emitter for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0a9a2848a5b7feac301353437eb7d5957887edbf81d56e903999a75a3d743086"},
+    {file = "PyYAML-6.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:29717114e51c84ddfba879543fb232a6ed60086602313ca38cce623c1d62cfbf"},
+    {file = "PyYAML-6.0.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:8824b5a04a04a047e72eea5cec3bc266db09e35de6bdfe34c9436ac5ee27d237"},
+    {file = "PyYAML-6.0.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:7c36280e6fb8385e520936c3cb3b8042851904eba0e58d277dca80a5cfed590b"},
+    {file = "PyYAML-6.0.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ec031d5d2feb36d1d1a24380e4db6d43695f3748343d99434e6f5f9156aaa2ed"},
+    {file = "PyYAML-6.0.2-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:936d68689298c36b53b29f23c6dbb74de12b4ac12ca6cfe0e047bedceea56180"},
+    {file = "PyYAML-6.0.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:23502f431948090f597378482b4812b0caae32c22213aecf3b55325e049a6c68"},
+    {file = "PyYAML-6.0.2-cp310-cp310-win32.whl", hash = "sha256:2e99c6826ffa974fe6e27cdb5ed0021786b03fc98e5ee3c5bfe1fd5015f42b99"},
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+    {file = "PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3ad2a3decf9aaba3d29c8f537ac4b243e36bef957511b4766cb0057d32b0be85"},
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+    {file = "PyYAML-6.0.2-cp312-cp312-win_amd64.whl", hash = "sha256:7e7401d0de89a9a855c839bc697c079a4af81cf878373abd7dc625847d25cbd8"},
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+    {file = "PyYAML-6.0.2-cp313-cp313-musllinux_1_1_aarch64.whl", hash = "sha256:41e4e3953a79407c794916fa277a82531dd93aad34e29c2a514c2c0c5fe971cc"},
+    {file = "PyYAML-6.0.2-cp313-cp313-musllinux_1_1_x86_64.whl", hash = "sha256:68ccc6023a3400877818152ad9a1033e3db8625d899c72eacb5a668902e4d652"},
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+    {file = "PyYAML-6.0.2-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:d84a1718ee396f54f3a086ea0a66d8e552b2ab2017ef8b420e92edbc841c352d"},
+    {file = "PyYAML-6.0.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9056c1ecd25795207ad294bcf39f2db3d845767be0ea6e6a34d856f006006083"},
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+    {file = "PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3b1fdb9dc17f5a7677423d508ab4f243a726dea51fa5e70992e59a7411c89d19"},
+    {file = "PyYAML-6.0.2-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:0b69e4ce7a131fe56b7e4d770c67429700908fc0752af059838b1cfb41960e4e"},
+    {file = "PyYAML-6.0.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:a9f8c2e67970f13b16084e04f134610fd1d374bf477b17ec1599185cf611d725"},
+    {file = "PyYAML-6.0.2-cp39-cp39-win32.whl", hash = "sha256:6395c297d42274772abc367baaa79683958044e5d3835486c16da75d2a694631"},
+    {file = "PyYAML-6.0.2-cp39-cp39-win_amd64.whl", hash = "sha256:39693e1f8320ae4f43943590b49779ffb98acb81f788220ea932a6b6c51004d8"},
+    {file = "pyyaml-6.0.2.tar.gz", hash = "sha256:d584d9ec91ad65861cc08d42e834324ef890a082e591037abe114850ff7bbc3e"},
+]
+
+[[package]]
+name = "virtualenv"
+version = "20.26.5"
+description = "Virtual Python Environment builder"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "virtualenv-20.26.5-py3-none-any.whl", hash = "sha256:4f3ac17b81fba3ce3bd6f4ead2749a72da5929c01774948e243db9ba41df4ff6"},
+    {file = "virtualenv-20.26.5.tar.gz", hash = "sha256:ce489cac131aa58f4b25e321d6d186171f78e6cb13fafbf32a840cee67733ff4"},
+]
+
+[package.dependencies]
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<5"
+
+[package.extras]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
+
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11.4"
-content-hash = "0e9c7de1a14ab89ba216b00deb52b83bda978915d965f459b3bfce8f2b6f5d77"
+content-hash = "aa9362db1f4605a8d183a481eed9b3763b2a3382b38f9ed4a3989ee82a70c1c6"
diff --git a/pyproject.toml b/pyproject.toml
index a70546a..a2943cf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,6 +8,9 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.11.4"
+
+[tool.poetry.group.dev.dependencies]
+pre-commit = "^3.8.0"
 pytest = "^8.3.3"
 
 [tool.ruff]

From 6e4c3dc34b4e8504b4504f3176134b552076f372 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 27 Sep 2024 11:49:03 +0200
Subject: [PATCH 18/21] Add authors

---
 CheckQC/pyproject.toml            | 2 +-
 GenderCheck/pyproject.toml        | 2 +-
 MosaicHunter/1.0.0/pyproject.toml | 2 +-
 pyproject.toml                    | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CheckQC/pyproject.toml b/CheckQC/pyproject.toml
index ea711c4..402d9e6 100644
--- a/CheckQC/pyproject.toml
+++ b/CheckQC/pyproject.toml
@@ -2,7 +2,7 @@
 name = "checkqc"
 version = "0.1.0"
 description = "Check and judge qc metrics (files)"
-authors = ["Your Name <you@example.com>"]
+authors = ["Bioinformatica Genetica <bioinformatica-genetica@umcutrecht.nl>"]
 license = 'MIT'
 package-mode = false
 
diff --git a/GenderCheck/pyproject.toml b/GenderCheck/pyproject.toml
index 3c87838..9a4d458 100644
--- a/GenderCheck/pyproject.toml
+++ b/GenderCheck/pyproject.toml
@@ -2,7 +2,7 @@
 name = "gendercheck"
 version = "0.1.0"
 description = ""
-authors = ["Your Name <you@example.com>"]
+authors = ["Bioinformatica Genetica <bioinformatica-genetica@umcutrecht.nl>"]
 license = "MIT"
 package-mode = false
 
diff --git a/MosaicHunter/1.0.0/pyproject.toml b/MosaicHunter/1.0.0/pyproject.toml
index f98b9a7..7b74836 100644
--- a/MosaicHunter/1.0.0/pyproject.toml
+++ b/MosaicHunter/1.0.0/pyproject.toml
@@ -2,7 +2,7 @@
 name = "mosaichunter"
 version = "1.0.0"
 description = ""
-authors = ["Your Name <you@example.com>"]
+authors = ["Bioinformatica Genetica <bioinformatica-genetica@umcutrecht.nl>"]
 license = "MIT"
 package-mode = false
 
diff --git a/pyproject.toml b/pyproject.toml
index a2943cf..67a3fbd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,7 @@
 name = "custommodules"
 version = "0.1.0"
 description = "custom nextflow processes and their linked files"
-authors = ["Your Name <you@example.com>"]
+authors = ["Bioinformatica Genetica <bioinformatica-genetica@umcutrecht.nl>"]
 license = "MIT"
 readme = "README.md"
 

From 940044c15725f56b270e8b9bc53d813836db1164 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Mon, 30 Sep 2024 08:12:38 +0200
Subject: [PATCH 19/21] filter paths on push

---
 .github/workflows/checkqc_lint.yml       | 1 +
 .github/workflows/checkqc_test.yml       | 1 +
 .github/workflows/gendercheck_lint.yml   | 1 +
 .github/workflows/gendercheck_test.yml   | 1 +
 .github/workflows/moisaichunter_lint.yml | 1 +
 .github/workflows/moisaichunter_test.yml | 1 +
 6 files changed, 6 insertions(+)

diff --git a/.github/workflows/checkqc_lint.yml b/.github/workflows/checkqc_lint.yml
index fcd49e9..26629c5 100644
--- a/.github/workflows/checkqc_lint.yml
+++ b/.github/workflows/checkqc_lint.yml
@@ -3,6 +3,7 @@ on:
   pull_request:
     paths: [CheckQC/**]
   push:
+    paths: [CheckQC/**]
     branches: [master, develop]
 
 jobs:
diff --git a/.github/workflows/checkqc_test.yml b/.github/workflows/checkqc_test.yml
index 2ab9133..7073f49 100644
--- a/.github/workflows/checkqc_test.yml
+++ b/.github/workflows/checkqc_test.yml
@@ -4,6 +4,7 @@ on:
   pull_request:
     paths: [CheckQC/**]
   push:
+    paths: [CheckQC/**]
     branches: [master, develop]
 
 jobs:
diff --git a/.github/workflows/gendercheck_lint.yml b/.github/workflows/gendercheck_lint.yml
index cece608..e848061 100644
--- a/.github/workflows/gendercheck_lint.yml
+++ b/.github/workflows/gendercheck_lint.yml
@@ -3,6 +3,7 @@ on:
   pull_request:
     paths: [GenderCheck/**]
   push:
+    paths: [GenderCheck/**]
     branches: [master, develop]
 
 jobs:
diff --git a/.github/workflows/gendercheck_test.yml b/.github/workflows/gendercheck_test.yml
index f92821a..4ff1d82 100644
--- a/.github/workflows/gendercheck_test.yml
+++ b/.github/workflows/gendercheck_test.yml
@@ -4,6 +4,7 @@ on:
   pull_request:
     paths: [GenderCheck/**]
   push:
+    paths: [GenderCheck/**]
     branches: [master, develop]
 
 jobs:
diff --git a/.github/workflows/moisaichunter_lint.yml b/.github/workflows/moisaichunter_lint.yml
index 5742c9d..96d6c07 100644
--- a/.github/workflows/moisaichunter_lint.yml
+++ b/.github/workflows/moisaichunter_lint.yml
@@ -3,6 +3,7 @@ on:
   pull_request:
     paths: [MosaicHunter/**]
   push:
+    paths: [MosaicHunter/**]
     branches: [master, develop]
 
 jobs:
diff --git a/.github/workflows/moisaichunter_test.yml b/.github/workflows/moisaichunter_test.yml
index c88aab0..44471f3 100644
--- a/.github/workflows/moisaichunter_test.yml
+++ b/.github/workflows/moisaichunter_test.yml
@@ -4,6 +4,7 @@ on:
   pull_request:
     paths: [MosaicHunter/**]
   push:
+    paths: [MosaicHunter/**]
     branches: [master, develop]
 
 jobs:

From da9f31df4e3d34c5214ce79d8accd162e13bb1a6 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Mon, 30 Sep 2024 08:14:24 +0200
Subject: [PATCH 20/21] move filter paths on push one row down.

---
 .github/workflows/checkqc_lint.yml       | 2 +-
 .github/workflows/checkqc_test.yml       | 2 +-
 .github/workflows/gendercheck_lint.yml   | 2 +-
 .github/workflows/gendercheck_test.yml   | 2 +-
 .github/workflows/moisaichunter_lint.yml | 2 +-
 .github/workflows/moisaichunter_test.yml | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/checkqc_lint.yml b/.github/workflows/checkqc_lint.yml
index 26629c5..6c153c0 100644
--- a/.github/workflows/checkqc_lint.yml
+++ b/.github/workflows/checkqc_lint.yml
@@ -3,8 +3,8 @@ on:
   pull_request:
     paths: [CheckQC/**]
   push:
-    paths: [CheckQC/**]
     branches: [master, develop]
+    paths: [CheckQC/**]
 
 jobs:
   ruff:
diff --git a/.github/workflows/checkqc_test.yml b/.github/workflows/checkqc_test.yml
index 7073f49..fd9b320 100644
--- a/.github/workflows/checkqc_test.yml
+++ b/.github/workflows/checkqc_test.yml
@@ -4,8 +4,8 @@ on:
   pull_request:
     paths: [CheckQC/**]
   push:
-    paths: [CheckQC/**]
     branches: [master, develop]
+    paths: [CheckQC/**]
 
 jobs:
   pytest:
diff --git a/.github/workflows/gendercheck_lint.yml b/.github/workflows/gendercheck_lint.yml
index e848061..79a1150 100644
--- a/.github/workflows/gendercheck_lint.yml
+++ b/.github/workflows/gendercheck_lint.yml
@@ -3,8 +3,8 @@ on:
   pull_request:
     paths: [GenderCheck/**]
   push:
-    paths: [GenderCheck/**]
     branches: [master, develop]
+    paths: [GenderCheck/**]
 
 jobs:
   ruff:
diff --git a/.github/workflows/gendercheck_test.yml b/.github/workflows/gendercheck_test.yml
index 4ff1d82..b5083d4 100644
--- a/.github/workflows/gendercheck_test.yml
+++ b/.github/workflows/gendercheck_test.yml
@@ -4,8 +4,8 @@ on:
   pull_request:
     paths: [GenderCheck/**]
   push:
-    paths: [GenderCheck/**]
     branches: [master, develop]
+    paths: [GenderCheck/**]
 
 jobs:
   pytest:
diff --git a/.github/workflows/moisaichunter_lint.yml b/.github/workflows/moisaichunter_lint.yml
index 96d6c07..dd00c08 100644
--- a/.github/workflows/moisaichunter_lint.yml
+++ b/.github/workflows/moisaichunter_lint.yml
@@ -3,8 +3,8 @@ on:
   pull_request:
     paths: [MosaicHunter/**]
   push:
-    paths: [MosaicHunter/**]
     branches: [master, develop]
+    paths: [MosaicHunter/**]
 
 jobs:
   ruff:
diff --git a/.github/workflows/moisaichunter_test.yml b/.github/workflows/moisaichunter_test.yml
index 44471f3..f1906d0 100644
--- a/.github/workflows/moisaichunter_test.yml
+++ b/.github/workflows/moisaichunter_test.yml
@@ -4,8 +4,8 @@ on:
   pull_request:
     paths: [MosaicHunter/**]
   push:
-    paths: [MosaicHunter/**]
     branches: [master, develop]
+    paths: [MosaicHunter/**]
 
 jobs:
   pytest:

From 740e504ae22d43dd2178f70522a4fcc4c2102000 Mon Sep 17 00:00:00 2001
From: ellendejong <de.jong.ellen@hotmail.com>
Date: Fri, 11 Oct 2024 10:36:08 +0200
Subject: [PATCH 21/21] Use poetry to run pytest

---
 .github/workflows/gendercheck_test.yml   |  3 +-
 .github/workflows/moisaichunter_test.yml |  3 +-
 CheckQC/checkqc_giabeval_settings.yaml   | 64 ++++++++++++++++++++++++
 3 files changed, 66 insertions(+), 4 deletions(-)
 create mode 100644 CheckQC/checkqc_giabeval_settings.yaml

diff --git a/.github/workflows/gendercheck_test.yml b/.github/workflows/gendercheck_test.yml
index b5083d4..dc3d279 100644
--- a/.github/workflows/gendercheck_test.yml
+++ b/.github/workflows/gendercheck_test.yml
@@ -59,5 +59,4 @@ jobs:
       #----------------------------------------------
       - name: Run tests
         run: |
-          source .venv/bin/activate
-          pytest .
+          poetry run pytest .
diff --git a/.github/workflows/moisaichunter_test.yml b/.github/workflows/moisaichunter_test.yml
index f1906d0..6cd3467 100644
--- a/.github/workflows/moisaichunter_test.yml
+++ b/.github/workflows/moisaichunter_test.yml
@@ -59,5 +59,4 @@ jobs:
       #----------------------------------------------
       - name: Run tests
         run: |
-          source .venv/bin/activate
-          pytest .
+          poetry run pytest .
diff --git a/CheckQC/checkqc_giabeval_settings.yaml b/CheckQC/checkqc_giabeval_settings.yaml
new file mode 100644
index 0000000..39bf986
--- /dev/null
+++ b/CheckQC/checkqc_giabeval_settings.yaml
@@ -0,0 +1,64 @@
+metrics:
+  - filename: "summary_snp.*truth.txt"
+    qc_col: "Sensitivity"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "Sensitivity"]
+    sample_cols: ["sample_1"]
+    title: "PK_C_SNPs"
+  - filename: "summary_indel.*truth.txt"
+    qc_col: "Sensitivity"
+    threshold: 0.90
+    operator: "<="
+    report_cols: ["sample_1", "Sensitivity"]
+    sample_cols: ["sample_1"]
+    title: "PK_C_INDELs"
+  - filename: "summary_snp.*truth.txt"
+    qc_col: "Precision"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "Precision"]
+    sample_cols: ["sample_1"]
+    title: "PK_D_SNPs"
+  - filename: "summary_indel.*truth.txt"
+    qc_col: "Precision"
+    threshold: 0.85
+    operator: "<="
+    report_cols: ["sample_1", "Precision"]
+    sample_cols: ["sample_1"]
+    title: "PK_D_INDELs"
+  - filename: "summary_snp_.*_((?!truth).)*$"
+    qc_col: "Sensitivity"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "sample_2", "Sensitivity"]
+    sample_cols: ["sample_1", "sample_2"]
+    title: "PK_E_SNPs"
+  - filename: "summary_indel_.*_((?!truth).)*$"
+    qc_col: "Sensitivity"
+    threshold: 0.90
+    operator: "<="
+    report_cols: ["sample_1", "sample_2", "Sensitivity"]
+    sample_cols: ["sample_1", "sample_2"]
+    title: "PK_E_INDELs"
+  - filename: "summary_high_conf_snp.*truth.txt"
+    qc_col: "Sensitivity"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "Sensitivity"]
+    sample_cols: ["sample_1"]
+    title: "PK_C_SNPs_high_conf"
+  - filename: "summary_high_conf_snp.*truth.txt"
+    qc_col: "Precision"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "Precision"]
+    sample_cols: ["sample_1"]
+    title: "PK_D_SNPs_high_conf"
+  - filename: "summary_high_conf_snp_.*_((?!truth).)*$"
+    qc_col: "Sensitivity"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "sample_2", "Sensitivity"]
+    sample_cols: ["sample_1", "sample_2"]
+    title: "PK_E_SNPs_high_conf"
\ No newline at end of file