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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:
# TODO: add in other test profiles
germline_wes:
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_wes
enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline_wes ) }}
env:
# TODO: parse this out somehow
pipeline_version: 3.1.1test
steps:
- name: Download pipeline
uses: actions/checkout@v4
- name: Download files from AWS
uses: keithweaver/[email protected]
if: ${{ matrix.enabled }}
with:
# TODO: download all vcfs
source: s3://nf-core-awsmegatests/sarek/results-test-59026dc07633edb83aab3bfb2f65f79db38437a1/test_full/variant_calling/strelka
command: sync
aws_region: eu-west-1
destination: ./variant_calling
flags: --no-sign-request --include ".vcf.gz" --exclude "g.vcf.gz"
# TOD remove this, it is probably not needed anymore, we are using python now
#- name: Create new Zenodo entry
# uses: popperized/zenodo/create@master
# env:
# ZENODO_METADATA_PATH: sarek-ncbench/assets/zenodo_ncbench.json
# entrypoint:
# secrets: ${{ secrets.ZENODO_DEPOSIT }}
#
#- name: Upload file to Zenodo
# uses: popperized/zenodo/upload@master
# env:
# ZENODO_UPLOAD_PATH: ./variant_calling
- name: Install requests
run: pip install requests # version pinning?
- name: Upload to zenodo
env:
ACCESS_TOKEN: ${{ secrets.ZENODO_DEPOSIT }}
run: |
python .github/workflows/upload.py
# 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: Add entry to config
uses: mikefarah/yq@master
with:
# TODO: add in values for all callers, ensure proper extension for the datasets are used. Parse out tool versions somehow
# TODO: need to retrieve new zenodo id
cmd: yq --inplace '
with(.variant-calls.nf-core-sarek-321-strelka-agilent-75M.labels;
.site = "nf-core" |
.pipeline = "nf-core/sarek v3.2.1" |
.trimming = "FastP v0.23.2" |
.read-mapping = "bwa mem v0.7.17" |
.base-quality-recalibration = "gatk4 v4.4.0.0" |
.realignment = "none" |
.variant-detection = "strelka2 v2.9.10" |
.genotyping = "none" |
.reads = "75M" ) |
with(.variant-calls.nf-core-sarek-321-strelka-agilent-75M.subcategory;
. = "NA12878-agilent" ) |
with(.variant-calls.nf-core-sarek-321-strelka-agilent-75M.zenodo;
.deposition = "get here proper zenodo ID" |
.filename = "get here proper file names" ) |
with(.variant-calls.nf-core-sarek-321-strelka-agilent-75M.benchmark;
. = "giab-NA12878-agilent-75M" ) |
with(.variant-calls.nf-core-sarek-321-strelka-agilent-75M.rename-contigs;
. = "resources/rename-contigs/ucsc-to-ensembl.txt" )
' ncbench-workflow/config/config.yaml
# TODO: enable using secrets here
- name: Commit files
run: |
cd ncbench-workflow
git config --global user.email "[email protected]"
git config --global user.name "FriederikeHanssen"
git checkout -b test6
git add config/config.yaml
git commit -a -m "Add changes"
git push origin test6