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@weber8thomas
weber8thomas committed Jun 22, 2024
2 parents 6005072 + 360282c commit 4d2e843
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82 changes: 0 additions & 82 deletions .github/workflows/assemblies.yaml
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name: MosaiCatcher assemblies checks

on:
schedule:
# Run every Sunday at 00:00 UTC on the master branch
- cron: "0 0 * * 0"
# branches:
# - master
push:
branches:
- "*"
- "!master"
- "!dev"
jobs:
# Downloading_example_data:
# runs-on: ubuntu-latest
# # needs:
# # - Linting
# # - Formatting
# steps:
# - uses: actions/checkout@v3.3.0
# - name: Downloading_example_data
# uses: snakemake/snakemake-github-action@v1.24.0
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# stagein: "mamba install -c conda-forge unzip"
# args: "--cores 1 --config dl_bam_example=True -p --verbose --debug"

Downloading_hg19:
runs-on: ubuntu-latest
# needs:
# - Linting
# - Formatting
steps:
- uses: actions/checkout@v3.3.0
- name: Downloading hg19
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 --conda-frontend mamba --config reference=hg19 -p --verbose --debug workflow/data/ref_genomes/config/BSgenome_hg19.ok"
Downloading_hg38:
runs-on: ubuntu-latest # needs:
# - Linting
# - Formatting
steps:
- uses: actions/checkout@v3.3.0
- name: Downloading hg38
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 --conda-frontend mamba --config reference=hg38 -p --verbose --debug workflow/data/ref_genomes/config/BSgenome_hg38.ok"
Downloading_T2T:
runs-on: ubuntu-latest # needs:
# - Linting
# - Formatting
steps:
- uses: actions/checkout@v3.3.0
- name: Downloading T2T
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 --conda-frontend mamba --latency-wait 60 --config reference=T2T -p --verbose --debug workflow/data/ref_genomes/config/BSgenome_T2T.ok"
Downloading_mm10:
runs-on: ubuntu-latest # needs:
# - Linting
# - Formatting
steps:
- uses: actions/checkout@v3.3.0
- name: Downloading T2T
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 --conda-frontend mamba --latency-wait 60 --config reference=mm10 -p --verbose --debug workflow/data/ref_genomes/config/BSgenome_mm10.ok"
297 changes: 0 additions & 297 deletions .github/workflows/conda.yaml
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name: MosaiCatcher conda checks

on:
schedule:
# Run every Sunday at 00:00 UTC on the master branch
- cron: "0 0 * * 0"
# branches:
# - master
push:
branches:
- "*"
- "!master"
- "!dev"

jobs:
# WORK

Testing_norm_disabled:
runs-on: ubuntu-latest
# needs:
# - Linting
# - Formatting
steps:
- uses: actions/checkout@v3.3.0
- 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config hgsvc_based_normalized_counts=False --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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config hgsvc_based_normalized_counts=False --conda-frontend mamba --report report.zip"

Linting_ashleys:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3.3.0
- 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
# needs:
# - Linting
# - Formatting
steps:
- uses: actions/checkout@v3.3.0
- 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True --conda-frontend mamba --report report.zip"

# Testing_ashleys_multistep_norm:
# runs-on: ubuntu-latest
# # needs:
# # - Linting
# # - Formatting
# steps:
# - uses: actions/checkout@v3.3.0
# - 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True multistep_normalisation=True --conda-frontend mamba --report report.zip"
# Testing_ashleys_multistep_norm_for_SV_calling:
# runs-on: ubuntu-latest
# # needs:
# # - Linting
# # - Formatting
# steps:
# - uses: actions/checkout@v3.3.0
# - 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True multistep_normalisation=True hgsvc_based_normalized_counts=False multistep_normalisation_for_SV_calling=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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True multistep_normalisation=True hgsvc_based_normalized_counts=False multistep_normalisation_for_SV_calling=True --conda-frontend mamba --report report.zip"
# Testing_ashleys_norm_counts_disabled:
# runs-on: ubuntu-latest
# # needs:
# # - Linting
# # - Formatting
# steps:
# - uses: actions/checkout@v3.3.0
# - 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True hgsvc_based_normalized_counts=False --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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True hgsvc_based_normalized_counts=False --conda-frontend mamba --report report.zip"
# # Testing_ashleys_norm_enabled_multistep_normalisation:
# # runs-on: ubuntu-latest
# # # needs:
# # # - Linting
# # # - Formatting
# # steps:
# # - uses: actions/checkout@v3.3.0
# # - 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config chromosomes=[chr17] ashleys_pipeline=True hgsvc_based_normalized_counts=True multistep_normalisation=True use_light_data=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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config chromosomes=[chr17] ashleys_pipeline=True hgsvc_based_normalized_counts=True multistep_normalisation=True use_light_data=True --conda-frontend mamba --report report.zip"
# # Testing_ashleys_jup_nb:
# # runs-on: ubuntu-latest
# # # needs:
# # # - Linting
# # # - Formatting
# # steps:
# # - uses: actions/checkout@v3.3.0
# # - 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True hand_selection=True --conda-frontend mamba --report report.zip"

# # Testing_ashleys_norm_enabled_hg19:
# # runs-on: ubuntu-latest
# # # needs:
# # # - Linting
# # # - Formatting
# # steps:
# # - uses: actions/checkout@v3.3.0
# # - 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 --latency-wait 60 --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] hgsvc_based_normalized_counts=True reference=hg19 --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 --latency-wait 60 --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] hgsvc_based_normalized_counts=True reference=hg19 --conda-frontend mamba --report report.zip"
# # Testing_ashleys_norm_enabled_hg38_full:
# # runs-on: ubuntu-latest
# # # needs:
# # # - Linting
# # # - Formatting
# # steps:
# # - uses: actions/checkout@v3.3.0
# # - 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 --latency-wait 60 --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] hgsvc_based_normalized_counts=True reference=hg38 --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 --latency-wait 60 --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] hgsvc_based_normalized_counts=True reference=hg38 --conda-frontend mamba --report report.zip"
# # Testing_ashleys_norm_enabled_T2T:
# # runs-on: ubuntu-latest
# # # needs:
# # # - Linting
# # # - Formatting
# # steps:
# # - uses: actions/checkout@v3.3.0
# # - 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 --latency-wait 60 --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] hgsvc_based_normalized_counts=True reference=T2T --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 --latency-wait 60 --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] hgsvc_based_normalized_counts=True reference=T2T --conda-frontend mamba --report report.zip"
# # Testing_ashleys_norm_enabled_mmconda --latency-wait 60 --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] hgsvc_based_normalized_counts=True reference=mm10 --conda-frontend mamba --report report.zip"
# Linting_arbigent:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v3.3.0
# - name: Linting
# uses: snakemake/snakemake-github-action@v1.24.0
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# args: "--lint --config arbigent=True"
# Testing_arbigent:
# runs-on: ubuntu-latest
# # needs:
# # - Linting
# # - Formatting
# steps:
# - uses: actions/checkout@v3.3.0
# - 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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config arbigent=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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config arbigent=True --conda-frontend mamba -p --verbose --debug --report report.zip"

# Testing_publishdir:
# runs-on: ubuntu-latest
# # needs:
# # - Linting
# # - Formatting
# steps:
# - uses: actions/checkout@v3.3.0
# - 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 --latency-wait 60 --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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba -p --verbose --debug --report report.zip"
# Downloading_extracting_scNOVA_data:
# runs-on: ubuntu-latest

# # needs:
# # - Linting
# # - Formatting
# steps:
# - uses: actions/checkout@v3.3.0
# - name: Downloading & extracting scNOVA 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 --conda-frontend mamba --verbose --debug workflow/data/scNOVA/utils/bin_Genes_for_CNN_reshape_annot.txt -p --latency-wait 120"
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