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fix: remove -r flag #624

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merged 2 commits into from
Jan 16, 2024
Merged

fix: remove -r flag #624

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10bb203
remove -r flag
alethomas Jan 2, 2024
808475a
fix
alethomas Jan 2, 2024
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14 changes: 7 additions & 7 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ jobs:
#- Pre-Commit
strategy:
matrix:
rule: [all, all -npr]
rule: [all, all -np]
# disable ont actions
technology: [all, illumina, ont, ion]
# technology: [all, illumina, ion]
Expand Down Expand Up @@ -141,26 +141,26 @@ jobs:
with:
directory: .tests
snakefile: workflow/Snakefile
args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
args: "-p --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"

- name: Test report
uses: snakemake/[email protected]
if: startsWith(matrix.rule, 'all -npr') != true
if: startsWith(matrix.rule, 'all -np') != true
with:
directory: .tests
snakefile: workflow/Snakefile
args: "${{ matrix.rule }} --report report.zip"

- name: Upload report
uses: actions/upload-artifact@v3
if: matrix.technology == 'all' && matrix.rule != 'all -npr'
if: matrix.technology == 'all' && matrix.rule != 'all -np'
with:
name: report-rule-${{ matrix.rule }}-${{ matrix.technology }}-${{ matrix.seq_method }}
path: .tests/results/patient-reports/2022-01-01.zip

- name: Upload logs
uses: actions/upload-artifact@v3
if: matrix.technology == 'all' && matrix.rule != 'all -npr'
if: matrix.technology == 'all' && matrix.rule != 'all -np'
with:
name: log-rule-${{ matrix.rule }}-technology-${{ matrix.technology }}
path: .tests/logs/
Expand Down Expand Up @@ -319,11 +319,11 @@ jobs:
with:
directory: .tests
snakefile: workflow/Snakefile
args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
args: "-p --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"

- name: Test report
uses: snakemake/[email protected]
if: startsWith(matrix.rule, 'all -npr') != true
if: startsWith(matrix.rule, 'all -np') != true
with:
directory: .tests
snakefile: workflow/Snakefile
Expand Down
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