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ncbench.yml
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name: NCBench Zenodo Upload
# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
on:
# upload can only be triggered manually for now
workflow_dispatch:
inputs:
germline_default_agilent:
description: "Trigger NCBench upload"
type: boolean
default: true
pull_request: # TODO: remove once it works
jobs:
ncbench-upload:
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
include:
# TODO: Add in other test profiles
- profile: germline_default_agilent
enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline_default_agilent ) }}
steps:
- name: Download pipeline
uses: actions/checkout@v4
- name: Extract Versions
id: extract_versions
run: |
PIPELINE_VERSION=$(awk -F"'" '/manifest {/,/version/ {if(/version/) print $2}' nextflow.config)
echo "PIPELINE_VERSION=${PIPELINE_VERSION}" >> $GITHUB_ENV
echo "PIPELINE_VERSION_NO_DOTS=$(echo $PIPELINE_VERSION | tr -d '.')" >> $GITHUB_ENV
FASTP_VERSION=$(awk '/- bioconda::fastp=/ {gsub(/.*=/, "", $NF); gsub(/'\''/, "", $NF); print $NF}' modules/nf-core/fastp/environment.yml)
echo "FASTP_VERSION=${FASTP_VERSION}" >> $GITHUB_ENV
BWA_VERSION=$(awk '/- bwa=/ {gsub(/.*=/, "", $NF); gsub(/'\''/, "", $NF); print $NF}' modules/nf-core/bwa/mem/environment.yml)
echo "BWA_VERSION=${BWA_VERSION}" >> $GITHUB_ENV
BQSR_VERSION=$(awk '/- bioconda::gatk4=/ {gsub(/.*=/, "", $NF); gsub(/'\''/, "", $NF); print $NF}' modules/nf-core/gatk4/baserecalibrator/environment.yml)
echo "BQSR_VERSION=${BQSR_VERSION}" >> $GITHUB_ENV
DEEPVARIANT_VERSION=$(awk -F':' '/container/ {gsub(/"/, "", $2); print $2}' modules/nf-core/deepvariant/main.nf)
echo "DEEPVARIANT_VERSION=${DEEPVARIANT_VERSION}" >> $GITHUB_ENV
FREEBAYES_VERSION=$(awk '/- bioconda::freebayes=/ {gsub(/.*=/, "", $NF); gsub(/'\''/, "", $NF); print $NF}' modules/nf-core/freebayes/environment.yml)
echo "FREEBAYES_VERSION=${FREEBAYES_VERSION}" >> $GITHUB_ENV
HAPLOTYPECALLER_VERSION=$(awk '/- bioconda::gatk4=/ {gsub(/.*=/, "", $NF); gsub(/'\''/, "", $NF); print $NF}' modules/nf-core/gatk4/haplotypecaller/environment.yml)
echo "HAPLOTYPECALLER_VERSION=${HAPLOTYPECALLER_VERSION}" >> $GITHUB_ENV
STRELKA_VERSION=$(awk '/- bioconda::strelka=/ {gsub(/.*=/, "", $NF); gsub(/'\''/, "", $NF); print $NF}' modules/nf-core/strelka/germline/environment.yml)
echo "STRELKA_VERSION=${STRELKA_VERSION}" >> $GITHUB_ENV
- name: Download files from AWS
uses: keithweaver/[email protected]
if: ${{ matrix.enabled }}
with:
# TODO: fix path to agilent test path
source: "s3://nf-core-awsmegatests/sarek/results-4bfb25049fdd2bf31c751bafcb6a18eddebcc1d5/test_full_germline_ncbench_agilent/variant_calling" #"s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/test_full_germline_ncbench_agilent/variant_calling"
command: sync
aws_region: eu-west-1
destination: ./variant_calling
flags: --no-sign-request --include ".vcf.gz" --exclude "g.vcf.gz"
- name: Install requests
run: pip install requests
- name: Upload to zenodo
id: upload_zenodo
env:
# ATTENTION: Use SANDBOX TOKEN during development: ${{ secrets.NCBENCH_CI_TOKEN_SANDBOX }}
ACCESS_TOKEN: ${{ secrets.NCBENCH_CI_TOKEN_SANDBOX }} # ${{ secrets.ZENODO_DEPOSIT }}
PIPELINE_VERSION: ${{ env.PIPELINE_VERSION }}
run: python .github/workflows/upload.py
- name: Store Zenodo deposition ID
run: |
echo "DEPOSITION_ID=$(cat deposition_id.txt)" >> $GITHUB_ENV
# update ncbench config yml
- name: NCBench set config
uses: actions/checkout@v4
with:
token: ${{ secrets.NCBENCH_CI_TOKEN }}
repository: FriederikeHanssen/ncbench-workflow
path: ncbench-workflow/
ref: main
- name: Install yq
uses: mikefarah/yq@master
- name: Add entry to config
env:
PIPELINE_VERSION_NO_DOTS: ${{ env.PIPELINE_VERSION_NO_DOTS}}
PIPELINE_VERSION: ${{ env.PIPELINE_VERSION }}
FASTP_VERSION: ${{ env.FASTP_VERSION }}
BWA_VERSION: ${{ env.BWA_VERSION }}
BQSR_VERSION: ${{ env.BQSR_VERSION }}
DEEPVARIANT_VERSION: ${{ env.DEEPVARIANT_VERSION }}
FREEBAYES_VERSION: ${{ env.FREEBAYES_VERSION }}
HAPLOTYPECALLER_VERSION: ${{ env.HAPLOTYPECALLER_VERSION }}
STRELKA_VERSION: ${{ env.STRELKA_VERSION }}
DEPOSITION_ID: ${{ env.DEPOSITION_ID }}
run: bash .github/workflows/set_ncbench_config.sh
- name: Commit files
uses: EndBug/add-and-commit@v7
with:
cwd: "./ncbench-workflow"
author: "FriederikeHanssen <[email protected]>"
new_branch: "sarek_${{ env.PIPELINE_VERSION }}"
message: "Add changes"
add: "ncbench-workflow/config/config.yaml"