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Add first two modules (diamond and kaiju), missing docs and tests #1

Add first two modules (diamond and kaiju), missing docs and tests

Add first two modules (diamond and kaiju), missing docs and tests #1

Workflow file for this run

# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
name: nf-core CI
on:
push:
branches:
- "dev"
pull_request:
branches:
- "dev"
- "master"
release:
types:
- "published"
env:
NXF_ANSI_LOG: false
NFTEST_VER: "0.7.3"
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
define_nxf_versions:
name: Choose nextflow versions to test against depending on target branch
runs-on: ubuntu-latest
outputs:
matrix: ${{ steps.nxf_versions.outputs.matrix }}
steps:
- id: nxf_versions
run: |
if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
else
echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
fi
test:
name: nf-test
needs: define_nxf_versions
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
tags:
- "test"
profile:
- "docker"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Check out test data
uses: actions/checkout@v3
with:
repository: nf-core/test-datasets
ref: createtaxdb
path: test-datasets/
fetch-depth: 1
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Install nf-test
run: |
wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
sudo mv nf-test /usr/local/bin/
- name: Run nf-test
run: |
nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: always() # always run even if the previous step fails
with:
report_paths: "*.xml"