New ivar_variants_to_vcf.py #176
Workflow file for this run
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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 | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
test: | |
name: Run pipeline with test data | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
NXF_VER: | |
- "23.04.0" | |
- "latest-everything" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
- name: Free some space | |
run: | | |
sudo rm -rf /usr/share/dotnet | |
sudo rm -rf /opt/ghc | |
sudo rm -rf "/usr/local/share/boost" | |
- name: Free Disk Space (Ubuntu) | |
uses: jlumbroso/[email protected] | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Disk space cleanup | |
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
- name: Run pipeline with test data | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --publish_dir_mode link --outdir ./results | |
parameters: | |
name: Test workflow parameters | |
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
parameters: | |
- "--consensus_caller ivar" | |
- "--variant_caller bcftools --consensus_caller ivar" | |
- "--skip_fastp --skip_pangolin" | |
- "--skip_variants" | |
- "--skip_cutadapt --skip_snpeff" | |
- "--skip_kraken2" | |
- "--skip_assembly" | |
- "--spades_mode corona" | |
- "--spades_mode metaviral" | |
- "--skip_plasmidid false --skip_asciigenome" | |
- "--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Free some space | |
run: | | |
sudo rm -rf /usr/share/dotnet | |
sudo rm -rf /opt/ghc | |
sudo rm -rf "/usr/local/share/boost" | |
- name: Free Disk Space (Ubuntu) | |
uses: jlumbroso/[email protected] | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Download GTF for additional annotation | |
if: contains(matrix.parameters, 'additional_annotation') | |
run: | | |
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz | |
- name: Run pipeline with various parameters | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --publish_dir_mode link --outdir ./results | |
test_sispa: | |
name: Test SISPA workflow | |
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
parameters: | |
- "--gff false" | |
- "--genome 'NC_045512.2'" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Run pipeline with minimal SISPA data and various options | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }} --outdir ./results | |
test_nanopore: | |
name: Test Nanopore workflow | |
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
parameters: | |
- "--gff false" | |
- "--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz" | |
- "--input false" | |
- "--min_barcode_reads 10000" | |
- "--min_guppyplex_reads 10000" | |
- "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false" | |
- "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false --artic_minion_medaka_model ./r941_min_high_g360_model.hdf5" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Download GTF for additional annotation | |
if: contains(matrix.parameters, 'additional_annotation') | |
run: | | |
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz | |
- name: Download medaka model | |
if: contains(matrix.parameters, 'r941_min_high_g360_model.hdf5') | |
run: | | |
wget https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g360_model.hdf5 | |
- name: Run pipeline with minimal Nanopore data and various options | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }} --outdir ./results |