Skip to content

Commit

Permalink
Merge pull request #55 from friendsofstrandseq/weber8thomas/bug-slurm…
Browse files Browse the repository at this point in the history 
…-time

Fix bug slurm time
  • Loading branch information
@weber8thomas
weber8thomas authored Jul 1, 2024
2 parents d83cdc3 + d5d7232 commit 8e7567c
Show file tree
Hide file tree
Showing 6 changed files with 309 additions and 289 deletions.
16 changes: 8 additions & 8 deletions .github/workflows/docker.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,14 @@ on:
- info
- warning
- debug
tags:
description: "Test scenario tags"
required: false
type: boolean
environment:
description: "Environment to run tests against"
type: environment
required: true
# tags:
# description: "Test scenario tags"
# required: false
# type: boolean
# environment:
# description: "Environment to run tests against"
# type: environment
# required: true

jobs:
build_container:
Expand Down
265 changes: 0 additions & 265 deletions .github/workflows/main_test.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -158,268 +158,3 @@ jobs:
# run: |
# snakemake -j 1 -c 1 --executor slurm --workflow-profile .tests/config/slurm_config/ \
# --use-conda --conda-frontend mamba --configfile .tests/config/simple_config_ashleys.yaml -p --snakefile workflow/Snakefile

Testing-with-MultiQC:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic
steps:
- name: Checkout repository with submodules
uses: actions/[email protected]
with:
submodules: recursive

# Update references
- name: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"

- 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==7.32.4

- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml --config MultiQC=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-ms-norm:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic
steps:
- name: Checkout repository with submodules
uses: actions/[email protected]
with:
submodules: recursive

# Update references
- name: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"

- 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==7.32.4

- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml --config multistep_normalisation=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-hg38:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules
uses: actions/[email protected]
with:
submodules: recursive

# Update references
- name: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"

- 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==7.32.4

- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-hg19:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules
uses: actions/[email protected]
with:
submodules: recursive

# Update references
- name: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"

- 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==7.32.4

- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-T2T:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules
uses: actions/[email protected]
with:
submodules: recursive

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

- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"

- 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==7.32.4

- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-mm10:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules
uses: actions/[email protected]
with:
submodules: recursive

# Update references
- name: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"

- 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==7.32.4

- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing_publishdir:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/[email protected]
# - name: Testing data
# uses: snakemake/[email protected]
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# stagein: "conda config --set channel_priority flexible"
# args: "--cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba -p --verbose --debug"
# - name: Testing report
# uses: snakemake/[email protected]
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# args: "--cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba --report report.zip"
Loading

0 comments on commit 8e7567c

Please sign in to comment.