update scripts with file-sync #14
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| name: update scripts with file-sync | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| # At 03:03 on Tuesday | |
| - cron: '3 3 * * 2' | |
| jobs: | |
| sync: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - run: ./.github/sync.sh liulab-dfci/TRUST4 BuildImgtAnnot.pl inst/extdata/TRUST4/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update TRUST4: BuildImgtAnnot.pl" | |
| - run: ./.github/sync.sh liulab-dfci/TRUST4 BuildDatabaseFa.pl inst/extdata/TRUST4/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update TRUST4: BuildDatabaseFa.pl" | |
| - run: ./.github/sync.sh sjdlabgroup/SAHMI functions/kreport2mpa.py inst/extdata/kraken2/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update kraken2: kreport2mpa.py" | |
| - run: ./.github/sync.sh jenniferlu717/KrakenTools combine_kreports.py inst/extdata/KrakenTools/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update KrakenTools: combine_kreports.py" | |
| - run: ./.github/sync.sh jenniferlu717/KrakenTools combine_mpa.py inst/extdata/KrakenTools/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update KrakenTools: combine_mpa.py" | |
| - run: ./.github/sync.sh jenniferlu717/KrakenTools extract_kraken_reads.py inst/extdata/KrakenTools/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update KrakenTools: extract_kraken_reads.py" | |
| - run: ./.github/sync.sh jenniferlu717/KrakenTools filter_bracken.out.py inst/extdata/KrakenTools/filter_bracken_out.py | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update KrakenTools: filter_bracken.out.py" | |
| - run: ./.github/sync.sh jenniferlu717/KrakenTools fix_unmapped.py inst/extdata/KrakenTools/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update KrakenTools: fix_unmapped.py" | |
| - run: ./.github/sync.sh jenniferlu717/KrakenTools kreport2krona.py inst/extdata/KrakenTools/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update KrakenTools: kreport2krona.py" | |
| - run: ./.github/sync.sh jenniferlu717/KrakenTools kreport2mpa.py inst/extdata/KrakenTools/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update KrakenTools: kreport2mpa.py" | |
| - run: ./.github/sync.sh jenniferlu717/KrakenTools make_kreport.py inst/extdata/KrakenTools/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update KrakenTools: make_kreport.py" | |
| - run: ./.github/sync.sh jenniferlu717/KrakenTools make_ktaxonomy.py inst/extdata/KrakenTools/ | |
| - uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "update KrakenTools: make_ktaxonomy.py" |