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Add button for manual test trigger #26

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Merged
hdbeukel merged 4 commits into from
May 21, 2025
Merged

Add button for manual test trigger #26

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e705feb
Update test.yml
hdbeukel May 12, 2025
ae2f5e4
Use Docker instead of Singularity for automated tests
May 12, 2025
14e89d4
Skip Singularity setup as now using Docker instead
May 12, 2025
89ea74f
Follow redirects with curl to download test data
May 12, 2025
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14 changes: 5 additions & 9 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ on:
branches: [ "main", "dev" ]
pull_request:
branches: [ "main", "dev" ]
workflow_dispatch:

jobs:
nf-test:
Expand All @@ -28,20 +29,15 @@ jobs:
- name: Setup Nextflow
uses: nf-core/setup-nextflow@v1.3.0

- 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
curl -k -L -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 -L -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 -L -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 -L -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
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7 changes: 1 addition & 6 deletions tests/nextflow.config
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Expand Up @@ -5,12 +5,7 @@
*/

process.container = "vibpsb/mini-ac:latest"
singularity {
enabled = true
cacheDir = "singularity_cache"
autoMounts = true
runOptions = "--bind %TMP%"
}
docker.enabled = true

workDir = "%TMP%/MINI-AC"

Expand Down