refactor: adjust final report; add full region scanning in CSM #239
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| ############################################################################### | |
| # | |
| # GitHub Actions CI configuration for integration tests | |
| # | |
| # AUTHOR: Maciej_Bak | |
| # AFFILIATION: University_of_Basel | |
| # AFFILIATION: Swiss_Institute_of_Bioinformatics | |
| # CONTACT: [email protected] | |
| # CREATED: 14-12-2021 | |
| # LICENSE: Apache_2.0 | |
| # | |
| ############################################################################### | |
| --- | |
| name: integration | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| PQA-module: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Create snakemake DAG | |
| run: | | |
| bash modules/PREPROCESSING/execution/run.sh \ | |
| -c .test/integration/module_PQA/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/PREPROCESSING/Snakefile \ | |
| --configfile=.test/integration/module_PQA/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| - name: Build conda envs for all the rules | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/PREPROCESSING/Snakefile \ | |
| --configfile=.test/integration/module_PQA/config.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| ASE-module: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Create snakemake DAG | |
| run: | | |
| bash modules/EXTRACT_AS_EXONS/execution/run.sh \ | |
| -c .test/integration/module_ASE/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/EXTRACT_AS_EXONS/Snakefile \ | |
| --configfile=.test/integration/module_ASE/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| - name: Build conda envs for all the rules | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/EXTRACT_AS_EXONS/Snakefile \ | |
| --configfile=.test/integration/module_ASE/config.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| TPA-module: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Create snakemake DAG | |
| run: | | |
| bash modules/PREPARE_TANDEM_PAS/execution/run.sh \ | |
| -c .test/integration/module_TPA/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/PREPARE_TANDEM_PAS/Snakefile \ | |
| --configfile=.test/integration/module_TPA/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| - name: Build conda envs for all the rules | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/PREPARE_TANDEM_PAS/Snakefile \ | |
| --configfile=.test/integration/module_TPA/config.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| QEI-module: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Create snakemake DAG | |
| run: | | |
| bash modules/QUANTIFICATION/execution/run.sh \ | |
| -c .test/integration/module_QEI/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/QUANTIFICATION/Snakefile \ | |
| --configfile=.test/integration/module_QEI/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| - name: Build conda envs for all the rules | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/QUANTIFICATION/Snakefile \ | |
| --configfile=.test/integration/module_QEI/config.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| PAQ-module: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Create snakemake DAG | |
| run: | | |
| bash modules/PAQR/execution/run.sh \ | |
| -c .test/integration/module_PAQ/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/PAQR/Snakefile \ | |
| --configfile=.test/integration/module_PAQ/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| - name: Build conda envs for all the rules | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/PAQR/Snakefile \ | |
| --configfile=.test/integration/module_PAQ/config.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| CSM-module: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| # Test 1: kmers | |
| - name: "Test 1: Create snakemake DAG" | |
| run: | | |
| bash modules/CREATE_SITECOUNT_MATRICES/execution/run.sh \ | |
| -c .test/integration/module_CSM/config1_kmers.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| # | |
| - name: "Test 1: Initiate snakemake dry run" | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/CREATE_SITECOUNT_MATRICES/Snakefile \ | |
| --configfile=.test/integration/module_CSM/config1_kmers.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| # | |
| - name: "Test 1: Build conda envs for all the rules" | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/CREATE_SITECOUNT_MATRICES/Snakefile \ | |
| --configfile=.test/integration/module_CSM/config1_kmers.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| # Test 2: pwms | |
| - name: "Test 2: Create snakemake DAG" | |
| run: | | |
| bash modules/CREATE_SITECOUNT_MATRICES/execution/run.sh \ | |
| -c .test/integration/module_CSM/config2_pwms.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| # | |
| - name: "Test 2: Initiate snakemake dry run" | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/CREATE_SITECOUNT_MATRICES/Snakefile \ | |
| --configfile=.test/integration/module_CSM/config2_pwms.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| # | |
| - name: "Test 2: Build conda envs for all the rules" | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/CREATE_SITECOUNT_MATRICES/Snakefile \ | |
| --configfile=.test/integration/module_CSM/config2_pwms.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| MAE-module: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Create snakemake DAG | |
| run: | | |
| bash modules/MAEI/execution/run.sh \ | |
| -c .test/integration/module_MAE/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/MAEI/Snakefile \ | |
| --configfile=.test/integration/module_MAE/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| - name: Build conda envs for all the rules | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/MAEI/Snakefile \ | |
| --configfile=.test/integration/module_MAE/config.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| KPC-module: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Create snakemake DAG | |
| run: | | |
| bash modules/KAPAC/execution/run.sh \ | |
| -c .test/integration/module_KPC/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/KAPAC/Snakefile \ | |
| --configfile=.test/integration/module_KPC/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| - name: Build conda envs for all the rules | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/KAPAC/Snakefile \ | |
| --configfile=.test/integration/module_KPC/config.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| RES-module: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Create snakemake DAG | |
| run: | | |
| bash modules/REPORT_RESULTS/execution/run.sh \ | |
| -c .test/integration/module_RES/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/REPORT_RESULTS/Snakefile \ | |
| --configfile=.test/integration/module_RES/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| - name: Build conda envs for all the rules | |
| run: | | |
| snakemake \ | |
| --snakefile=modules/REPORT_RESULTS/Snakefile \ | |
| --configfile=.test/integration/module_RES/config.yml \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 8 | |
| MAPP-test1: | |
| needs: | |
| - PQA-module | |
| - ASE-module | |
| - TPA-module | |
| - QEI-module | |
| - PAQ-module | |
| - CSM-module | |
| - MAE-module | |
| - KPC-module | |
| - RES-module | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Download genomic resources | |
| run: | | |
| bash scripts/download-ENSEMBL-resources.sh \ | |
| --species hsa \ | |
| --output-directory resources_ENSEMBL_hsa | |
| - name: Download the atlas of PolyA sites | |
| run: | | |
| bash scripts/download-polyA-atlas.sh \ | |
| --species hsa \ | |
| --output-directory ATLAS2_hsa | |
| - name: Download and parse ATtRACT motifs | |
| run: | | |
| bash scripts/download-and-parse-ATtRACT-motifs.sh \ | |
| --output-directory ATtRACT_hsa | |
| - name: Create the main configfile | |
| run: | | |
| python scripts/create-main-config-file.py \ | |
| --config-template .test/integration/MAPP/config_template_1.yml \ | |
| --pipeline-configfile configs/config.yml | |
| - name: Create snakemake rulegraph | |
| run: | | |
| bash execution/run.sh \ | |
| -c configs/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g rulegraph rulegraph.svg | |
| - name: Create snakemake DAG | |
| run: | | |
| bash execution/run.sh \ | |
| -c configs/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=Snakefile \ | |
| --configfile=configs/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| MAPP-test2: | |
| needs: | |
| - PQA-module | |
| - ASE-module | |
| - TPA-module | |
| - QEI-module | |
| - PAQ-module | |
| - CSM-module | |
| - MAE-module | |
| - KPC-module | |
| - RES-module | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout mapp repository | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda & mapp main environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| activate-environment: mapp | |
| environment-file: env/environment.yml | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Download genomic resources | |
| run: | | |
| bash scripts/download-ENSEMBL-resources.sh \ | |
| --species hsa \ | |
| --output-directory resources_ENSEMBL_hsa | |
| - name: Download the atlas of PolyA sites | |
| run: | | |
| bash scripts/download-polyA-atlas.sh \ | |
| --species hsa \ | |
| --output-directory ATLAS2_hsa | |
| - name: Download and parse ATtRACT motifs | |
| run: | | |
| bash scripts/download-and-parse-ATtRACT-motifs.sh \ | |
| --output-directory ATtRACT_hsa | |
| # for this test it is required that we set the | |
| # modification date of resources files as older than | |
| # the pipeline files (expected situation): | |
| - name: Adjust modification date for resources | |
| run: | | |
| touch -a -m -t 200001010000.00 resources_ENSEMBL_hsa/Homo_sapiens.GRCh38.102.gtf | |
| touch -a -m -t 200001010000.00 resources_ENSEMBL_hsa/Homo_sapiens.GRCh38.dna.primary_assembly.fa | |
| touch -a -m -t 200001010000.00 ATLAS2_hsa/reformatted_filtered_atlas.bed | |
| # according to the notes in the pipeline configuration: | |
| # comment-out ASE, TPA and CSM modules inclusion from the main Snakefile: | |
| - name: Comment-out ASE, TPA, CSM modules | |
| run: | | |
| sed '52 {s/^/#/}' -i Snakefile | |
| sed '53 {s/^/#/}' -i Snakefile | |
| sed '56 {s/^/#/}' -i Snakefile | |
| - name: Create the main configfile | |
| run: | | |
| python scripts/create-main-config-file.py \ | |
| --config-template .test/integration/MAPP/config_template_2.yml \ | |
| --pipeline-configfile configs/config.yml | |
| - name: Create snakemake rulegraph | |
| run: | | |
| bash execution/run.sh \ | |
| -c configs/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g rulegraph rulegraph.svg | |
| - name: Create snakemake DAG | |
| run: | | |
| bash execution/run.sh \ | |
| -c configs/config.yml \ | |
| -e local \ | |
| -t conda \ | |
| -g dag dag.svg | |
| - name: Initiate snakemake dry run | |
| run: | | |
| snakemake \ | |
| --snakefile=Snakefile \ | |
| --configfile=configs/config.yml \ | |
| --printshellcmds \ | |
| --dryrun \ | |
| --verbose | |
| ... |