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Bug/sex determination #328

Bug/sex determination

Bug/sex determination #328

Workflow file for this run

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
env:
NXF_ANSI_LOG: false
AWS_ACCESS_KEY_ID: ${{ secrets.UGENT_S3_ACCESS_KEY }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.UGENT_S3_SECRET_KEY }}
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test_all:
name: Run nf-test with ${{ matrix.test }}-${{ matrix.NXF_VER }}
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/structural') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.10.0"
- "latest-everything"
test:
- "pipeline_sv"
- "pipeline_cnv"
- "pipeline_repeats"
- "pipeline_duplicates"
- "pipeline_families"
- "bam_cnv_calling"
- "bam_prepare_samtools"
- "bam_repeat_estimation_expansionhunter"
- "bam_sv_calling"
- "bam_variant_calling_delly"
# - "bam_variant_calling_gridss"
- "bam_variant_calling_manta"
- "bam_variant_calling_qdnaseq"
- "bam_variant_calling_smoove"
- "bam_variant_calling_wisecondorx"
- "vcf_annotate_vep_annotsv_vcfanno"
- "vcf_concat_bcftools"
- "vcf_merge_callers_jasmine"
- "vcf_merge_family_jasmine"
steps:
- name: Free some space
run: |
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
- name: Check out pipeline code
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Install nf-test
run: |
conda install -c bioconda nf-test==0.8.4
- name: Run pipeline with test data
run: |
$CONDA/bin/nf-test test --tag ${{ matrix.test }} --junitxml=default.xml
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: always() # always run even if the previous step fails
with:
report_paths: "default.xml"
- name: Upload log file artifact
if: failure()
uses: actions/upload-artifact@v3
with:
name: nf-test-workdir
path: .nf-test/