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2.2.1: fixes #211

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2.2.1: fixes

2.2.1: fixes #211

Workflow file for this run

.github/workflows/conda.yaml at d6b796f
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"
jobs:
# WORK
Testing_norm_disabled:
runs-on: ubuntu-latest
# needs:
# - Linting
# - Formatting
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 --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/[email protected]
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/[email protected]
- name: Linting
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--lint --config ashleys_pipeline=True"
Testing_ashleys:
runs-on: ubuntu-latest
# needs:
# - Linting
# - Formatting
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 --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/[email protected]
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/[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 --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/[email protected]
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/[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 --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/[email protected]
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/[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 --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/[email protected]
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/[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 --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/[email protected]
# 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/[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 --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/[email protected]
# 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/[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 --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/[email protected]
# 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/[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 --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/[email protected]
# 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/[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 --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/[email protected]
# 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/[email protected]
- name: Linting
uses: snakemake/[email protected]
with:
directory: .
snakefile: ./workflow/Snakefile
args: "--lint --config arbigent=True"
Testing_arbigent:
runs-on: ubuntu-latest
# needs:
# - Linting
# - Formatting
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 --latency-wait 60 --configfile .tests/config/simple_config.yaml --config arbigent=True --conda-frontend mamba -p --verbose --debug"
- name: Testing report
uses: snakemake/[email protected]
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/[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 --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/[email protected]
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/[email protected]
- name: Downloading & extracting scNOVA data
uses: snakemake/[email protected]
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"