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ci.yaml
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# ==================================================================================================
# Header
# ==================================================================================================
name: CI
on:
pull_request:
push:
branches:
- master
- dev
# ==================================================================================================
# Jobs
# ==================================================================================================
jobs:
# ==========================================================================
# test
# ==========================================================================
test:
# if: ${{ false }} # disable for now
runs-on: ${{ matrix.os }}
defaults:
run:
# Need to specify the shell explicitly.
# https://github.com/marketplace/actions/setup-miniconda#important
# https://github.com/conda-incubator/setup-miniconda#use-a-default-shell
shell: bash -el {0}
# -------------------------------------------------------
# Matrix
# -------------------------------------------------------
strategy:
fail-fast: false
matrix:
os:
- ubuntu-latest
# - macos-latest
# - ubuntu-20.04
# - ubuntu-22.04
# - ubuntu-24.04
# - macos-12
# - macos-13
# - macos-14
# Test cases as listed in test/cases/*.txt
# We update them automatically when running the test/run.sh script, so that each time
# we have and run a new test case, it also appears here. The script to run this update
# is located in .github/workflows/update-cases.sh
case:
# CASES_BEGIN
- base
- calling-bcftools-1
- calling-bcftools-2
- calling-bcftools-3
- calling-bcftools-4
- calling-freebayes-1
- calling-freebayes-2
- calling-freebayes-3
- calling-haplotypecaller-1
- calling-haplotypecaller-2
- calling-haplotypecaller-3
- calling-haplotypecaller-4
- download
- duplicates-dedup-1
- duplicates-dedup-2
- hafpipe-1
- hafpipe-2
- hafpipe-3
- hafpipe-4
- mapping-bowtie2-1
- mapping-bowtie2-2
- mapping-bwa-aln-1
- mapping-bwa-aln-2
- mapping-bwa-aln-3
- mapping-bwa-aln-4
- mapping-bwa-mem-1
- mapping-bwa-mem2-1
- mapping-bwa-mem2-2
- mappings-table
- pileup-1
- trimming-adapterremoval-1
- trimming-adapterremoval-2
- trimming-adapterremoval-3
- trimming-cutadapt-1
- trimming-cutadapt-2
- trimming-fastp-1
- trimming-fastp-2
- trimming-fastp-3
- trimming-none
- trimming-seqprep-1
- trimming-seqprep-2
- trimming-skewer-1
- trimming-skewer-2
# CASES_END
installer:
# - conda
- mamba
include:
# Also test with other operating systems.
# For now, we just test the base case to see if it's generally working.
# This repeats one of the Ubuntu runs for the base case, but that's okay
# to keep it future proof when the default ubuntu-latest changes.
- os: ubuntu-20.04
case: base
- os: ubuntu-22.04
case: base
- os: ubuntu-24.04
case: base
- os: macos-12
case: base
- os: macos-13
case: base
# - os: macos-14
# case: base
# -------------------------------------------------------
# Steps
# -------------------------------------------------------
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Setup Conda
# uses: conda-incubator/[email protected]
uses: mamba-org/[email protected]
with:
# We need mamba here already, otherwise we run into
# https://github.com/conda-incubator/setup-miniconda/issues/262
# mamba-version: "*"
# python-version: 3.12
# channels: conda-forge,defaults
# channel-priority: true
# use-mamba: true
# environment-file: workflow/envs/grenepipe.yaml
# activate-environment: grenepipe
# We might need to replace the above, at least for now, due to instabilities in the action,
# see https://github.com/conda-incubator/setup-miniconda/issues/274#issue-1531425010
# If that changes again in the future, also change it below in the other jobs.
# miniforge-variant: Mambaforge
# miniforge-version: latest
# New workaround suggestion:
# https://github.com/conda-incubator/setup-miniconda/issues/292#issuecomment-1767669652
# Why is this stuff so broken all the time?
# miniforge-variant: Mambaforge
# miniforge-version: latest
# use-mamba: true
# channels: conda-forge,defaults
# environment-file: workflow/envs/grenepipe.yaml
# activate-environment: grenepipe
# Nope, the above also does not work, this time due to
# https://github.com/snakemake/snakemake/issues/3108
# So now we try to use a completely different setup, and hope that that works,
# at least for now...
micromamba-version: '1.5.8-0'
environment-file: workflow/envs/grenepipe.yaml
environment-name: grenepipe
init-shell: bash
post-cleanup: 'all'
# Manually create the conda env.
# Not needed at the moment, as the above setup works (if it works).
# Keeping this here for reference.
# - name: Install Conda Env
# shell: bash -el {0}
# run: |
# mamba env create -f workflow/envs/grenepipe.yaml -n grenepipe
# Then in the run step:
# conda activate grenepipe
# Run the test case.
- name: Run Test
run: |
conda info
mamba info
if [[ "${{ matrix.installer }}" == "conda" ]]; then
export GRENEPIPE_TESTS_NO_MAMBA=1
fi
./test/run.sh ${{ matrix.case }}
# Store a list of all files and sizes, for debugging.
- name: File Inventory
if: always()
run: |
mkdir -p test/out-${{ matrix.case }}/logs
ls -alFR test/out-${{ matrix.case }} > test/out-${{ matrix.case }}/logs/files.txt
ls -alFR test/reference >> test/out-${{ matrix.case }}/logs/files.txt
# Upload the log files as a GitHub Actions artifact
- name: Upload Logs
if: always()
uses: actions/upload-artifact@v4
with:
name: logs-test-${{ matrix.os }}-${{ matrix.case }}
path: |
test/out-${{ matrix.case }}/config.yaml
test/out-${{ matrix.case }}/test-run.log
test/out-${{ matrix.case }}/logs/
test/out-${{ matrix.case }}/.snakemake/log/
test/reference/logs/
test/reference/TAIR10_chr_all.dict
# ==========================================================================
# example
# ==========================================================================
example:
# if: ${{ false }} # disable for now
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -el {0}
# -------------------------------------------------------
# Matrix
# -------------------------------------------------------
strategy:
fail-fast: false
matrix:
os:
- ubuntu-20.04
- ubuntu-22.04
- ubuntu-24.04
- macos-12
- macos-13
# - macos-14
# -------------------------------------------------------
# Steps
# -------------------------------------------------------
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Setup Conda
# uses: conda-incubator/[email protected]
uses: mamba-org/[email protected]
with:
# mamba-version: "*"
# channels: conda-forge
# Need to use a different setup to get mamba to work, see above.
# miniforge-variant: Mambaforge
# miniforge-version: latest
# use-mamba: true
# channels: conda-forge,defaults
# environment-file: workflow/envs/grenepipe.yaml
# activate-environment: grenepipe
# Same as above, need a different setup here...
micromamba-version: '1.5.8-0'
environment-file: workflow/envs/grenepipe.yaml
environment-name: grenepipe
init-shell: bash
post-cleanup: 'all'
- name: Run Example
run: |
./example/prepare.sh
snakemake --use-conda --conda-frontend mamba --cores 4 --directory example/ 2>&1 | tee example/run.log
- name: Upload Logs
if: always()
uses: actions/upload-artifact@v4
with:
name: logs-example-${{ matrix.os }}
path: |
example/run.log
example/logs/
example/.snakemake/log/
# ==========================================================================
# envs
# ==========================================================================
envs:
# if: ${{ false }} # disable for now
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -el {0}
# -------------------------------------------------------
# Matrix
# -------------------------------------------------------
strategy:
fail-fast: false
matrix:
os:
- ubuntu-20.04
- ubuntu-22.04
- ubuntu-24.04
- macos-12
- macos-13
# - macos-14
installer:
# Conda is just waaaay to slow... some runs even exceed the GitHub Actions
# max runtime of 6h, so we have to deactivate it for now.
# - conda
- mamba
- micromamba
# -------------------------------------------------------
# Steps
# -------------------------------------------------------
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Setup Conda
uses: mamba-org/[email protected]
with:
# Trying another installer, see if that one finally works,
# and to test if both mamba and micromamba work for all envs.
# Any version from https://github.com/mamba-org/micromamba-releases
micromamba-version: '1.5.8-0'
environment-file: workflow/envs/grenepipe.yaml
environment-name: grenepipe
init-shell: bash
post-cleanup: 'all'
- name: Install Envs
shell: bash -el {0}
run: |
cd workflow/envs
for env in `ls *.yaml` ; do
name=${env%.yaml}
printf "\n" ; printf '=%.0s' {1..100}
printf "\n ${name}\n"
printf '=%.0s' {1..100} ; printf "\n\n"
if [[ "$name" = "grenepipe" ]]; then
echo "Skipping grenepipe"
continue
fi
if [[ ${{ matrix.os }} == macos* ]] && [[ "${name}" == *-linux ]]; then
echo "Skipping linux env on macos"
continue
fi
if [[ ${{ matrix.os }} == ubuntu* ]] && [[ "${name}" == *-macos ]]; then
echo "Skipping macos env on linux"
continue
fi
${{ matrix.installer }} env create -f ${env} -n ${name}
done