Initial project set up based on https://github.com/nvnieuwk/nft-bam

.editorconfig

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+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 2
+indent_style = space
+
+[**pom.xml]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset

.github/workflows/build-docs.yml

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+name: build docs
+on:
+  push:
+    branches: [main]
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # fetch all commits/branches
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - name: Obtain version from manifest
+        run: |
+          version=$(grep "moduleVersion" src/main/resources/META-INF/nf-test-plugin | sed -e s'/[^=]*=//')
+          [[ $version == *"dev"* ]] && pipeline_version="dev" || pipeline_version=$version
+          echo "pipeline_version=$pipeline_version" >> $GITHUB_ENV
+      - name: Setup git user
+        run: |
+          git config --global user.name "${{github.actor}}"
+          git config --global user.email "${{github.actor}}@users.noreply.github.com"
+      - uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - name: Install dependencies
+        run: pip install mkdocs-material pymdown-extensions pillow cairosvg mike
+      - name: Build docs
+        run: mike deploy --push --update-aliases ${{ env.pipeline_version }} latest
+      - name: Set default docs
+        run: mike set-default --push latest

.github/workflows/test.yml

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+name: Run plugin tests
+on:
+  push:
+  pull_request:
+    branches: [main]
+  merge_group:
+    types: [checks_requested]
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        JAVA_VERSION: ["11", "17", "21"]
+    steps:
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
+
+      - name: Setup Java ${{ matrix.JAVA_VERSION }}
+        uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4
+        with:
+          distribution: "temurin"
+          java-version: "${{ matrix.JAVA_VERSION }}"
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+
+      - name: Build plugin
+        run: ./build.sh
+
+      - name: Test the plugin
+        env:
+          NFT_DIFF: "pdiff"
+          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+        run: |
+          ./test.sh
+
+      - name: Clean up
+        if: always()
+        run: |
+          sudo rm -rf /home/ubuntu/tests/

.gitignore

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+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+/target/
+/.classpath
+/.project
+/.settings/
+/.nextflow/
+/.nf-test/
+
+# generated test data
+tests/no_index.fasta.fai

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - prettier@3.3.3
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec

.prettierignore

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+.DS_Store
+.nextflow*
+*.pyc
+data/
+dependency-reduced-pom.xml
+pom.xml
+results/
+testing*
+testing/
+work/

.prettierrc

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+{
+  "tabWidth": 2,
+  "useTabs": false,
+  "printWidth": 120
+}

CHANGELOG.md

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+# Changelog
+
+## dev
+
+### New features
+
+The first release of nft-utils
+
+### Fixes
+
+Fixes are written here

build.sh

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+#!/bin/bash
+
+mvn package
+
+echo "Built $(readlink -f target/nft-utils*.jar)"

bump-version.sh

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+version=$1
+if [ -z $version ]
+then
+    echo "Please provide a version"
+    exit 1
+fi
+sed -i -e "0,/<version>/{s/<version>.*<\\/version>/<version>$version<\\/version>/}" ./pom.xml
+sed -i -e "s/moduleVersion=.*/moduleVersion=$version/" ./src/main/resources/META-INF/nf-test-plugin
+
+if [[ $version != *dev ]]
+then
+    sed -i -e "s/load \"nft-utils@.*\"/load \"nft-utils@$version\"/" ./docs/index.md
+fi
+
+./build.sh

dependency-reduced-pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>com.nf-core</groupId>
+  <artifactId>nft-utils</artifactId>
+  <name>nft-utils</name>
+  <version>0.4.0dev</version>
+  <description>nf-test plugin to support SAM/BAM/CRAM formats</description>
+  <url>https://github.com/nf-core/nft-utils</url>
+  <licenses>
+    <license>
+      <name>MIT License</name>
+      <url>http://www.opensource.org/licenses/mit-license.php</url>
+    </license>
+  </licenses>
+  <scm>
+    <connection>scm:git:https://github.com/nf-core/nft-utils</connection>
+    <developerConnection>scm:git:ssh://github.com:nf-core/nft-utils.git</developerConnection>
+    <url>https://github.com/nf-core/nft-utils/tree/master</url>
+  </scm>
+  <build>
+    <plugins>
+      <plugin>
+        <artifactId>maven-shade-plugin</artifactId>
+        <version>3.5.2</version>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+  <properties>
+    <maven.compiler.release>${java.version}</maven.compiler.release>
+    <java.version>11</java.version>
+    <maven.compiler.source>${java.version}</maven.compiler.source>
+    <maven.compiler.target>${java.version}</maven.compiler.target>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <htsjdk.version>3.0.5</htsjdk.version>
+    <additionalparam>-Xdoclint:none</additionalparam>
+  </properties>
+</project>

docs/index.md

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+# nft-utils
+
+nft-utils is an nf-test plugin to provide additional functions and assertions that fall outside of the typical nf-test features. They were primarily developed by the nf-core community but should be applicable to any nf-tests.
+
+## Start using the plugin
+
+To start using the plugin please add it to your `nf-test.config` file:
+
+```groovy title="nf-test.config"
+config {
+    plugins {
+        load "nft-utils"
+    }
+}
+```
+
+It's a good idea to specify a version which you can do using the `@` symbol, however currently there are no releases:
+
+```groovy title="nf-test.config"
+config {
+    plugins {
+        load "nft-utils@0.1.0"
+    }
+}
+```
+
+Have a look at the [usage documentation](./usage.md) for more information on how to start working with the plugin.
+
+## Use a development version
+
+To use the development version, please do the following steps:
+
+- Clone the [nft-utils repository](https://github.com/nf-core/nft-utils)
+
+=== "HTTPS"
+
+    ```bash
+    git clone git@github.com:nf-core/nft-utils.git
+    ```
+
+=== "SSH"
+
+    ```bash
+    git clone https://github.com/nf-core/nft-utils.git
+    ```
+
+- Run the build script
+
+```bash
+./build.sh
+```
+
+- Add the jar location (visible at the end of the build script output) to the `nf-test.config` file
+
+```groovy title="nf-test.config"
+config {
+    plugins {
+        loadFromFile "full/path/to/the/plugin/jar"
+    }
+}
+```

docs/usage.md

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+# Usage
+
+TBC!

mkdocs.yml

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+site_name: nf-core/nft-utils
+repo_name: nf-core/nft-utils
+repo_url: https://github.com/nf-core/nft-utils
+site_url: https://nf-core.github.io/nft-utils
+
+nav:
+  - Home: index.md
+  - Usage: usage.md
+
+theme:
+  name: material
+  icon:
+    logo: octicons/checklist-16
+    repo: fontawesome/brands/github
+  palette:
+    # Palette toggle for dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      primary: custom
+      accent: custom
+      toggle:
+        icon: material/weather-sunny
+        name: Switch to light mode
+    # Palette toggle for light mode
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      primary: custom
+      accent: custom
+      toggle:
+        icon: material/weather-night
+        name: Switch to dark mode
+  font:
+    text: Inter
+  features:
+    - content.code.annotate
+    - content.code.copy
+    - navigation.instant
+    - navigation.top
+    - navigation.tracking
+    - navigation.sections
+    - navigation.footer
+    - search.share
+    - toc.follow
+
+markdown_extensions:
+  - attr_list
+  - md_in_html
+  - admonition
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
+  - pymdownx.tabbed:
+      alternate_style: true
+
+extra:
+  version:
+    provider: mike

nf-test.config

@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile ""
+
+}