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Merged
merged 6 commits into from
Oct 1, 2025
Merged

Skip conda tests that cannot be run due to lacking dependencies #2008

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a947ddb
Skip conda tests that cannot be run due to lacking dependencies
maxulysse Sep 30, 2025
4bee0dd
shards too
maxulysse Sep 30, 2025
e6bf9bb
simplify logic
maxulysse Sep 30, 2025
6fb1065
fix GHA
maxulysse Sep 30, 2025
5125663
should work
maxulysse Sep 30, 2025
384bfc4
Trigger Build
maxulysse Sep 30, 2025
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1 change: 1 addition & 0 deletions .github/actions/nf-test/action.yml
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I don't see how that would skip the conda tests 🤔

Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,7 @@ runs:
nf-test test \
--profile=+${{ inputs.profile }} \
$(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
$(if [ "${{ inputs.profile }}" == "conda" ]; then echo "--tag "conda""; fi) \
--ci \
--changed-since HEAD^ \
--verbose \
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -173,6 +173,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1990](https://github.com/nf-core/sarek/pull/1990) - Update parabricks/fq2bam to 4.5.1-1
- [2001](https://github.com/nf-core/sarek/pull/2001) - Remove lofreq VCF MD5sum - use summary
- [2007](https://github.com/nf-core/sarek/pull/2007) - Sort tools in test_full configs and add msisensor2
- [2008](https://github.com/nf-core/sarek/pull/2008) - Skip conda tests that cannot be run due to lacking dependencies

#### Fixed

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6 changes: 4 additions & 2 deletions tests/aligner-parabricks.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,8 @@ nextflow_pipeline {
tools: '',
wes : true,
],
gpu: true
gpu: true,
tag: "no_conda"
],
[
name: "-profile test --aligner parabricks --tools mutect2 --wes --input fastq_pair.csv",
Expand All @@ -28,7 +29,8 @@ nextflow_pipeline {
tools: 'mutect2',
wes : true,
],
gpu: true
gpu: true,
tag: "no_conda"
]
]

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5 changes: 5 additions & 0 deletions tests/lib/UTILS.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,11 @@ class UTILS {
tag scenario.tag
}

// Add conda tag if not provided or not no_conda
if (!scenario.tag || scenario.tag != "no_conda") {
tag "conda"
}

when {
params {
// Mandatory, as we always need an outdir
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1 change: 1 addition & 0 deletions tests/postprocess_concatenation.nf.test
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Expand Up @@ -17,6 +17,7 @@ nextflow_pipeline {
tools: 'freebayes,haplotypecaller'
],
include_freebayes_unfiltered: true,
tag: "no_conda"
]
]

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1 change: 1 addition & 0 deletions tests/postprocess_concatenation_normalization.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ nextflow_pipeline {
tools: 'freebayes,haplotypecaller'
],
include_freebayes_unfiltered: true,
tag: "no_conda"
]
]

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1 change: 1 addition & 0 deletions tests/postprocess_normalization.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ nextflow_pipeline {
tools: 'freebayes,haplotypecaller'
],
include_freebayes_unfiltered: true,
tag: "no_conda"
]
]

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10 changes: 7 additions & 3 deletions tests/variant_calling_deepvariant.nf.test
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Expand Up @@ -14,7 +14,8 @@ nextflow_pipeline {
input: "${projectDir}/tests/csv/3.0/mapped_single_cram.csv",
step: "variant_calling",
tools: 'deepvariant'
]
],
tag: "no_conda"
],
[
name: "-profile test --tools deepvariant --input tests/csv/3.0/mapped_single_cram.csv -stub",
Expand All @@ -23,6 +24,7 @@ nextflow_pipeline {
step: "variant_calling",
tools: 'deepvariant'
],
tag: "no_conda",
stub: true
],
[
Expand All @@ -32,7 +34,8 @@ nextflow_pipeline {
step: "variant_calling",
tools: 'deepvariant',
no_intervals: true
]
],
tag: "no_conda",
],
[
name: "-profile test --tools deepvariant --input tests/csv/3.0/mapped_single_cram.csv --no_intervals -stub",
Expand All @@ -42,7 +45,8 @@ nextflow_pipeline {
tools: 'deepvariant',
no_intervals: true
],
stub: true
stub: true,
tag: "no_conda"
]
]

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6 changes: 4 additions & 2 deletions tests/variant_calling_haplotypecaller.nf.test
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Expand Up @@ -42,7 +42,8 @@ nextflow_pipeline {
wes: true,
nucleotides_per_second: 20,
skip_tools: 'haplotypecaller_filter'
]
],
tag: "no_conda"
],
[
name: "-profile test --input mapped_single_bam.csv --tools haplotypecaller --step variant_calling --wes --nucleotides_per_second 20 --skip_tools haplotypecaller_filter --no_intervals",
Expand All @@ -54,7 +55,8 @@ nextflow_pipeline {
nucleotides_per_second: 20,
skip_tools: 'haplotypecaller_filter',
no_intervals: true
]
],
tag: "no_conda"
]
]

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6 changes: 4 additions & 2 deletions tests/variant_calling_sentieon_haplotypecaller.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,8 @@ nextflow_pipeline {
input: "${projectDir}/tests/csv/3.0/mapped_single_bam.csv",
tools: "sentieon_haplotyper",
step: "variant_calling"
]
],
tag: "no_conda"
],
[
name: "-profile test --tools sentieon_haplotyper --no_intervals",
Expand All @@ -23,7 +24,8 @@ nextflow_pipeline {
tools: "sentieon_haplotyper",
step: "variant_calling",
no_intervals: true
]
],
tag: "no_conda"
],
[
name: "-profile test --tools sentieon_haplotyper --skip_tools haplotyper_filter",
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