Trying to pull LFS in submodules #43

Workflow file for this run

.github/workflows/main_test.yaml at d4beada

	name: ashleys-qc-pipeline workflow checks

	on:
	push:
	branches:
	- "**"

	jobs:
	Linting:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository with submodules
	uses: actions/checkout@v4
	with:
	submodules: 'recursive' # Ensures all submodules are checked out
	lfs: true # Ensures LFS objects for the main repo are pulled

	- name: Pull LFS objects in submodules
	run: \|
	git submodule foreach --recursive 'git lfs pull'

	- name: Setup Python
	uses: actions/setup-python@v2

	- name: Add Conda to system path
	run: \|
	echo $CONDA/bin >> $GITHUB_PATH

	- name: Install dependencies
	run: \|
	conda install -c conda-forge mamba

	- name: Setup snakemake
	run: \|
	mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: List contents of .tests
	run: \|
	tree -h .tests

	- name: List contents of workflow/data
	run: \|
	tree -h workflow/data

	- name: Run Snakemake Lint
	run: \|
	snakemake --lint


	# Testing_ashleys_with_custom_python:
	# # runs-on: self-hosted
	# runs-on: ubuntu-latest
	# steps:
	# - name: Checkout repository with submodules and lfs
	# uses: actions/checkout@v4
	# with:
	# submodules: recursive
	# lfs: true
	# - name: Setup Python
	# uses: actions/setup-python@v2
	# - name: Add Conda to system path
	# run: \|
	# echo $CONDA/bin >> $GITHUB_PATH
	# - name: Install dependencies
	# run: \|
	# conda install -c conda-forge mamba
	# - name: Setup snakemake
	# run: \|
	# mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
	# - name: Run workflow
	# run: \|
	# snakemake --cores 1 --software-deployment-method conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

	# Setting_slurm_cluster:
	# runs-on: ubuntu-latest
	# # For the action to work, you have to supply a mysql
	# # service as defined below.
	# services:
	# mysql:
	# image: mysql:8.0
	# env:
	# MYSQL_ROOT_PASSWORD: root
	# ports:
	# - "8888:3306"
	# options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
	# steps:
	# - uses: actions/checkout@v3

	# - uses: koesterlab/setup-slurm-action@v1

	# - name: Checkout repository with submodules and lfs
	# uses: actions/checkout@v4
	# with:
	# submodules: recursive
	# lfs: true
	# - name: Setup Python
	# uses: actions/setup-python@v2
	# - name: Add Conda to system path
	# run: \|
	# echo $CONDA/bin >> $GITHUB_PATH
	# - name: Install dependencies
	# run: \|
	# conda install -c conda-forge mamba
	# - name: Setup snakemake
	# run: \|
	# mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http snakemake-executor-plugin-slurm
	# - name: Run workflow
	# run: \|
	# snakemake -j 1 -c 4 --executor slurm --workflow-profile .tests/config/slurm_config/ --software-deployment-method conda --conda-frontend mamba --configfile .tests/config/simple_config.yaml -p --snakefile workflow/Snakefile

	# WORK
	# Formatting:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4

	# - name: Formatting
	# uses: github/super-linter@v4
	# env:
	# VALIDATE_ALL_CODEBASE: false
	# DEFAULT_BRANCH: master
	# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	# VALIDATE_SNAKEMAKE_SNAKEFMT: true

	# Linting:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Linting
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--lint --config ashleys_pipeline=True"
	# Testing_ashleys:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba --report report.zip"

	# Testing_ashleys_fastqc_enabled:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config MultiQC=True --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config MultiQC=True --conda-frontend mamba --report report.zip"

	# Testing_ashleys_ms_norm_enabled:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config multistep_normalisation=True --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config multistep_normalisation=True --conda-frontend mamba --report report.zip"
	# Testing_ashleys_hg38:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
	# Testing_ashleys_hg19:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
	# Testing_ashleys_T2T:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
	# Testing_ashleys_mm10:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --config reference=mm10 use_light_data=True chromosomes=[chr17] --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --config reference=mm10 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
	# Testing_jub_nb:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config hand_selection=True --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config hand_selection=True --conda-frontend mamba --report report.zip"
	# Testing_publishdir:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# stagein: "conda config --set channel_priority flexible"
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba -p --verbose --debug"
	# - name: Testing report
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba --report report.zip"
	# Testing_list_commands:
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: Testing data
	# uses: snakemake/snakemake-github-action@v1.24.0
	# with:
	# directory: .
	# snakefile: ./workflow/Snakefile
	# args: "--cores 1 --config list_commands=True --verbose --debug"

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Trying to pull LFS in submodules #43

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Trying to pull LFS in submodules #43

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Workflow file for this run