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Removing stub option from nf-cmd in the test of pipeline-download #1436

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Apr 8, 2024
Merged

Removing stub option from nf-cmd in the test of pipeline-download #1436

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e04f7aa
Removing option -stub from nf-cmd in the test of pipeline-download
asp8200 Mar 14, 2024
7513b7b
Updating changelog
asp8200 Mar 14, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/download_pipeline.yml
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Expand Up @@ -69,4 +69,4 @@ jobs:
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local modules
- [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local subworkflows
- [#1360](https://github.com/nf-core/sarek/pull/1360) - Sync `TEMPLATE` with `tools` `2.11`
- [#1385](https://github.com/nf-core/sarek/pull/1385), [#1436](https://github.com/nf-core/sarek/pull/1436) - Sync `TEMPLATE` with `tools` `2.12`
- [#1408](https://github.com/nf-core/sarek/pull/1408), [#1412](https://github.com/nf-core/sarek/pull/1412) - Updating samtools to v1.19.2 - except in GATK/markduplicates. (Temporarily disabled nf-test for bwamem2/mem.)
- [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporarily disable sentieon related tests
- [#1419](https://github.com/nf-core/sarek/pull/1419) - Updating GATK to v4.5, and updating samtools to v1.19.2 in GATK/markduplicates.
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