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New ivar_variants_to_vcf.py script #171

New ivar_variants_to_vcf.py script

New ivar_variants_to_vcf.py script #171

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
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