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General: Update CI to test template pipelines with nf-test #3559

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Merged
merged 20 commits into from
May 8, 2025
Merged

General: Update CI to test template pipelines with nf-test #3559

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9f2259a
update CI to test template pipelines with nf-test
mirpedrol May 5, 2025
ff44f5e
[automated] Update CHANGELOG.md
nf-core-bot May 5, 2025
d12f634
update changelog
mirpedrol May 5, 2025
bb33fd2
cd pipeline directory
mirpedrol May 5, 2025
b28d445
checkout code with depth 0
mirpedrol May 5, 2025
974e9dc
clean up unused dir
mirpedrol May 5, 2025
5994784
add cd create-test-lint-wf
mirpedrol May 5, 2025
e451dbb
remove --changed-since
mirpedrol May 5, 2025
4e39007
remove profile test and --ci
mirpedrol May 5, 2025
99ca8a5
fix work dir and remove nf-test dir before linting
mirpedrol May 5, 2025
cdc8db0
remove more nf-test files before linting pipeline
mirpedrol May 5, 2025
3308934
Run the pipeline when nf-test is not available
mirpedrol May 5, 2025
2be2850
fix GHA conditionals
mirpedrol May 5, 2025
dd62c1e
generate nf-test snapshot for testing if not present
mirpedrol May 6, 2025
7d1e090
add default snapshot and update nftignore file
mirpedrol May 6, 2025
61a370e
fix nf-test on pipelines from a template
mirpedrol May 7, 2025
4ce7166
generate snapshots once
mirpedrol May 7, 2025
5d56105
add all snapshots
mirpedrol May 7, 2025
8f4b27b
Apply suggestions from code review
mirpedrol May 8, 2025
cb296bb
rename __snapshots__ to snapshots
mirpedrol May 8, 2025
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109 changes: 109 additions & 0 deletions .github/snapshots/adaptivecard.nf.test.snap
View file
Open in desktop
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{
"-profile test": {
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4,
null,
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"fastqc/SAMPLE1_PE_1_fastqc.html",
"fastqc/SAMPLE1_PE_1_fastqc.zip",
"fastqc/SAMPLE1_PE_2_fastqc.html",
"fastqc/SAMPLE1_PE_2_fastqc.zip",
"fastqc/SAMPLE2_PE_1_fastqc.html",
"fastqc/SAMPLE2_PE_1_fastqc.zip",
"fastqc/SAMPLE2_PE_2_fastqc.html",
"fastqc/SAMPLE2_PE_2_fastqc.zip",
"fastqc/SAMPLE3_SE_1_fastqc.html",
"fastqc/SAMPLE3_SE_1_fastqc.zip",
"fastqc/SAMPLE3_SE_2_fastqc.html",
"fastqc/SAMPLE3_SE_2_fastqc.zip",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
"multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
"multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
"multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
"multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
"multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
"multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_counts_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_fastqc.txt",
"multiqc/multiqc_data/multiqc_general_stats.txt",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
"multiqc/multiqc_plots",
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"multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
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"multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
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"fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870",
"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
"multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110",
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]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.03.1"
},
"timestamp": "2025-05-07T13:52:10.350817122"
}
}
109 changes: 109 additions & 0 deletions .github/snapshots/changelog.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,109 @@
{
"-profile test": {
"content": [
4,
null,
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"fastqc/SAMPLE1_PE_2_fastqc.html",
"fastqc/SAMPLE1_PE_2_fastqc.zip",
"fastqc/SAMPLE2_PE_1_fastqc.html",
"fastqc/SAMPLE2_PE_1_fastqc.zip",
"fastqc/SAMPLE2_PE_2_fastqc.html",
"fastqc/SAMPLE2_PE_2_fastqc.zip",
"fastqc/SAMPLE3_SE_1_fastqc.html",
"fastqc/SAMPLE3_SE_1_fastqc.zip",
"fastqc/SAMPLE3_SE_2_fastqc.html",
"fastqc/SAMPLE3_SE_2_fastqc.zip",
"multiqc",
"multiqc/multiqc_data",
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"multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
"multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
"multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
"multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
"multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
"multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_counts_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_fastqc.txt",
"multiqc/multiqc_data/multiqc_general_stats.txt",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
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"multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
"multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
"multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
"multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
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"multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
"multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
"multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
"multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
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],
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},
"timestamp": "2025-05-07T13:52:01.993722854"
}
}
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