iCREs-based GRN inference feature #52
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| name: MINI-AC test suite | |
| on: | |
| push: | |
| branches: [ "main", "dev" ] | |
| pull_request: | |
| branches: [ "main", "dev" ] | |
| jobs: | |
| nf-test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Prepare nf-test config file | |
| run: sed -i -e "s@%TMP%@${RUNNER_TEMP}@g" tests/nextflow.config | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: oracle | |
| java-version: 17 | |
| - name: Check Java version | |
| run: java -version | |
| - name: Setup Nextflow | |
| uses: nf-core/[email protected] | |
| - name: Setup singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.3 | |
| - name: Setup nf-test | |
| run: wget -qO- https://code.askimed.com/install/nf-test | bash | |
| - name: Fetch motif mapping files | |
| run: | | |
| curl -k -o tests/data/zma_v4_chr1/zma_v4_genome_wide_motif_mappings_chr1.bed https://floppy.psb.ugent.be/index.php/s/NekMYztyxEnsQiY/download/zma_v4_genome_wide_motif_mappings_chr1.bed | |
| curl -k -o tests/data/zma_v4_chr1/zma_v4_locus_based_motif_mappings_5kbup_1kbdown_chr1.bed https://floppy.psb.ugent.be/index.php/s/r2wQmFjPy79qSp7/download/zma_v4_locus_based_motif_mappings_5kbup_1kbdown_chr1.bed | |
| curl -k -o data/ath/ath_genome_wide_motif_mappings.bed https://floppy.psb.ugent.be/index.php/s/iaZPwdrRGe3YDdK/download/ath_genome_wide_motif_mappings.bed | |
| curl -k -o data/ath/ath_locus_based_motif_mappings_5kbup_1kbdown.bed https://floppy.psb.ugent.be/index.php/s/qcQ7KndzHaSpd9e/download/ath_locus_based_motif_mappings_5kbup_1kbdown.bed | |
| - name: Run nf-test | |
| shell: bash | |
| run: ./nf-test test |