Merge release/12.0.3 into dev #2751
Workflow file for this run
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| --- | |
| name: MIP CI code coverage | |
| "on": ["pull_request", "push"] | |
| jobs: | |
| coverage: | |
| name: MIP code coverage | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: shogo82148/actions-setup-perl@v1 | |
| with: | |
| perl-version: '5.26' | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| channels: bioconda, conda-forge | |
| - name: Set up perl | |
| run: | | |
| perl -V | |
| cpanm --quiet --notest --installdeps . | |
| cpanm --quiet --notest Devel::Cover::Report::Coveralls | |
| - name: Install bcftools in conda test env | |
| shell: bash -l {0} | |
| run: | | |
| conda create -n mip_ci --channel bioconda --channel conda-forge bcftools=1.9=ha228f0b_4 | |
| - name: Run MIP install test | |
| shell: bash -l {0} | |
| run: PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_install.test | |
| - name: Install MIP rare disease | |
| shell: bash -l {0} | |
| run: | | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl mip install --envn mip_ci --select_program mip_scripts | |
| - name: Run MIP unit tests | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mip_ci | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",+ignore,"prove",-coverage,statement,branch,condition,path,subroutine prove -lrs -f -j 2 t | |
| - name: Run MIP download test | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mip_ci | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_download.test | |
| - name: Run MIP analyse tests | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mip_ci | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_dragen_rd_dna.test | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_dna_panel.test | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_dna.test | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_dna_vcf_rerun.test | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_rna.test | |
| - name: Run MIP scripts tests | |
| shell: bash -l {0} | |
| run: | | |
| conda activate mip_ci | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_qccollect.test | |
| PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_vcfparser.test | |
| - name: Calculate coveralls | |
| run: | | |
| cover | |
| cover -report coveralls |