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Update all nf-tests to follow template v3.3.1 more closely #896

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Merged
d4straub merged 6 commits into from
Jun 16, 2025
Merged

Update all nf-tests to follow template v3.3.1 more closely #896

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cb3347e
update all tests to template
d4straub Jun 12, 2025
f3cb0e3
add snaps for test_failed and test_fasta
d4straub Jun 12, 2025
d9fe44f
add a bunch of snaps
d4straub Jun 12, 2025
6d67884
update two snaps
d4straub Jun 13, 2025
d1adc8a
fix qiime2_barplotvg
d4straub Jun 13, 2025
a3091b0
fix default.nf.test.snap
d4straub Jun 13, 2025
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#893](https://github.com/nf-core/ampliseq/pull/893) - Template update for nf-core/tools version 3.3.1
- [#893](https://github.com/nf-core/ampliseq/pull/893),[#896](https://github.com/nf-core/ampliseq/pull/896) - Template update for nf-core/tools version 3.3.1

### `Dependencies`

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2 changes: 1 addition & 1 deletion subworkflows/local/qiime2_barplotavg.nf
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Expand Up @@ -30,7 +30,7 @@ workflow QIIME2_BARPLOTAVG {
ch_versions_qiime2_barplotavg = ch_versions_qiime2_barplotavg.mix(QIIME2_FEATURETABLE_GROUP.out.versions)

//Barplot
QIIME2_BPAVG ( [], QIIME2_FEATURETABLE_GROUP.out.qza, ch_tax, 'average' )
QIIME2_BPAVG ( [], QIIME2_FEATURETABLE_GROUP.out.qza, ch_tax.collect(), 'average' )
ch_versions_qiime2_barplotavg = ch_versions_qiime2_barplotavg.mix(QIIME2_BPAVG.out.versions)

emit:
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131 changes: 31 additions & 100 deletions tests/default.nf.test
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Expand Up @@ -16,114 +16,45 @@ nextflow_pipeline {
then {
// stable_name: All files + folders in ${params.outdir}/ with a stable name
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
// stable_path: All files in ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')

assert workflow.success
assertAll(
{ assert workflow.success},
/* New syntax, is not satisfied
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_ampliseq_software_mqc_versions.yml"),
removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
stable_path
// Manually chosen files for content checks
path("$outputDir/overall_summary.tsv"),
path("$outputDir/asv_length_filter/").list(),
path("$outputDir/barrnap/ASV_seqs.ssu.fasta"),
path("$outputDir/barrnap/ASV_table.ssu.tsv"),
path("$outputDir/barrnap/rrna.arc.gff"),
path("$outputDir/barrnap/rrna.bac.gff"),
path("$outputDir/barrnap/rrna.euk.gff"),
path("$outputDir/barrnap/stats.ssu.tsv"),
path("$outputDir/barrnap/rrna.mito.gff"),
path("$outputDir/cutadapt/cutadapt_summary.tsv"),
path("$outputDir/dada2/ASV_seqs.fasta"),
path("$outputDir/dada2/ASV_table.tsv"),
path("$outputDir/dada2/ref_taxonomy.gtdb_R07-RS207.txt"),
path("$outputDir/dada2/DADA2_stats.tsv"),
path("$outputDir/dada2/DADA2_table.rds"),
path("$outputDir/dada2/DADA2_table.tsv"),
path("$outputDir/input/Samplesheet.tsv"),
path("$outputDir/input/Metadata.tsv"),
path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt"),
path("$outputDir/SBDI/dna.tsv"),
path("$outputDir/SBDI/emof.tsv"),
path("$outputDir/SBDI/event.tsv"),
path("$outputDir/vsearch_cluster/ASV_post_clustering_filtered.fna"),
path("$outputDir/vsearch_cluster/ASV_post_clustering_filtered.stats.tsv"),
path("$outputDir/vsearch_cluster/ASV_post_clustering_filtered.table.tsv")
).match() }
*/
// Old syntax, provisionally used
{ assert new File("$outputDir/pipeline_info/software_versions.yml").exists() },
{ assert snapshot(path("$outputDir/overall_summary.tsv")).match("overall_summary_tsv") },
{ assert snapshot(path("$outputDir/asv_length_filter/").list()).match("asv_length_filter") },
{ assert snapshot(path("$outputDir/barrnap/ASV_seqs.ssu.fasta"),
path("$outputDir/barrnap/ASV_table.ssu.tsv"),
path("$outputDir/barrnap/rrna.arc.gff"),
path("$outputDir/barrnap/rrna.bac.gff"),
path("$outputDir/barrnap/rrna.euk.gff"),
path("$outputDir/barrnap/stats.ssu.tsv"),
path("$outputDir/barrnap/rrna.mito.gff")).match("barrnap") },
{ assert new File("$outputDir/barrnap/summary.tsv").exists() },
{ assert snapshot(path("$outputDir/cutadapt/cutadapt_summary.tsv")).match("cutadapt") },
{ assert new File("$outputDir/cutadapt/assignTaxonomy.cutadapt.log").exists() },
{ assert new File("$outputDir/cutadapt/sampleID_1a.trimmed.cutadapt.log").exists() },
{ assert new File("$outputDir/cutadapt/sampleID_1.trimmed.cutadapt.log").exists() },
{ assert new File("$outputDir/cutadapt/sampleID_2a.trimmed.cutadapt.log").exists() },
{ assert new File("$outputDir/cutadapt/sampleID_2.trimmed.cutadapt.log").exists() },
{ assert snapshot(path("$outputDir/dada2/ASV_seqs.fasta"),
path("$outputDir/dada2/ASV_table.tsv"),
path("$outputDir/dada2/ref_taxonomy.gtdb_R07-RS207.txt"),
path("$outputDir/dada2/DADA2_stats.tsv"),
path("$outputDir/dada2/DADA2_table.rds"),
path("$outputDir/dada2/DADA2_table.tsv")).match("dada2") },
{ assert new File("$outputDir/dada2/ASV_tax.gtdb_R07-RS207.tsv").exists() },
{ assert new File("$outputDir/dada2/ASV_tax_species.gtdb_R07-RS207.tsv").exists() },
{ assert new File("$outputDir/fastqc/sampleID_1_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/sampleID_1_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/sampleID_1a_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/sampleID_1a_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/sampleID_2_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/sampleID_2_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/sampleID_2a_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/sampleID_2a_2_fastqc.html").exists() },
{ assert snapshot(path("$outputDir/input/Samplesheet.tsv"),
path("$outputDir/input/Metadata.tsv")).match("input") },
{ assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
{ assert new File("$outputDir/qiime2/abundance_tables/abs-abund-table-2.tsv").exists() },
{ assert new File("$outputDir/qiime2/abundance_tables/abs-abund-table-3.tsv").exists() },
{ assert new File("$outputDir/qiime2/abundance_tables/abs-abund-table-4.tsv").exists() },
{ assert new File("$outputDir/qiime2/abundance_tables/count_table_filter_stats.tsv").exists() },
{ assert new File("$outputDir/qiime2/abundance_tables/filtered-table.qza").exists() },
{ assert new File("$outputDir/qiime2/abundance_tables/feature-table.biom").exists() },
{ assert new File("$outputDir/qiime2/abundance_tables/feature-table.tsv").exists() },
{ assert new File("$outputDir/qiime2/input/rep-seqs.qza").exists() },
{ assert new File("$outputDir/qiime2/input/table.qza").exists() },
{ assert new File("$outputDir/qiime2/input/taxonomy.qza").exists() },
{ assert new File("$outputDir/qiime2/rel_abundance_tables/rel-table-2.tsv").exists() },
{ assert new File("$outputDir/qiime2/rel_abundance_tables/rel-table-3.tsv").exists() },
{ assert new File("$outputDir/qiime2/rel_abundance_tables/rel-table-4.tsv").exists() },
{ assert new File("$outputDir/qiime2/rel_abundance_tables/rel-table-ASV.tsv").exists() },
{ assert new File("$outputDir/qiime2/rel_abundance_tables/rel-table-ASV_with-DADA2-tax.tsv").exists() },
{ assert new File("$outputDir/qiime2/rel_abundance_tables/rel-table-ASV_with-QIIME2-tax.tsv").exists() },
{ assert new File("$outputDir/qiime2/representative_sequences/descriptive_stats.tsv").exists() },
{ assert new File("$outputDir/qiime2/representative_sequences/filtered-sequences.qza").exists() },
{ assert new File("$outputDir/qiime2/representative_sequences/rep-seq.fasta").exists() },
{ assert new File("$outputDir/qiime2/representative_sequences/seven_number_summary.tsv").exists() },
{ assert new File("$outputDir/qiime2/taxonomy/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-classifier.qza").exists() },
{ assert new File("$outputDir/qiime2/taxonomy/ref_taxonomy.txt").exists() },
{ assert new File("$outputDir/qiime2/taxonomy/taxonomy.tsv").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-badpairwise10-ASV/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-badpairwise10-level-2/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-badpairwise10-level-3/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-badpairwise10-level-4/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-mix8-ASV/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-mix8-level-2/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-mix8-level-3/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-mix8-level-4/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-treatment1-ASV/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-treatment1-level-2/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-treatment1-level-3/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/da_barplot/Category-treatment1-level-4/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc/differentials/Category-treatment1-level-4/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc_formula/da_barplot/Category-treatment1-ASV/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc_formula/differentials/Category-treatment1-ASV/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc_formula/da_barplot/Category-treatment1-level-4/index.html").exists() },
{ assert new File("$outputDir/qiime2/ancombc_formula/differentials/Category-treatment1-level-4/index.html").exists() },
{ assert snapshot(path("$outputDir/SBDI/dna.tsv"),
path("$outputDir/SBDI/emof.tsv"),
path("$outputDir/SBDI/event.tsv")).match("SBDI") },
{ assert new File("$outputDir/SBDI/annotation.tsv").exists() },
{ assert new File("$outputDir/SBDI/asv-table.tsv").exists() },
{ assert new File("$outputDir/summary_report/summary_report.html").exists() },
{ assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() },
{ assert new File("$outputDir/phyloseq/qiime2_phyloseq.rds").exists() },
{ assert new File("$outputDir/treesummarizedexperiment/dada2_TreeSummarizedExperiment.rds").exists() },
{ assert new File("$outputDir/treesummarizedexperiment/qiime2_TreeSummarizedExperiment.rds").exists() },
{ assert snapshot(path("$outputDir/vsearch_cluster/ASV_post_clustering_filtered.fna"),
path("$outputDir/vsearch_cluster/ASV_post_clustering_filtered.stats.tsv"),
path("$outputDir/vsearch_cluster/ASV_post_clustering_filtered.table.tsv")).match("vsearch_cluster") }
)
}
}
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