re-organize tests and use tags in ci job matrix

.gitattributes

@@ -1,4 +1,5 @@
 *.config linguist-language=nextflow
 *.nf.test linguist-language=nextflow
+tests/**/*nf.test.snap linguist-generated
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

.github/workflows/ci.yml

@@ -36,23 +36,25 @@ jobs:
           fi
 
   test:
-    name: Run pipeline with test data
+    name: nf-test
     needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
-        component:
-          - "tests/pipeline/misc/custom_reftax.nf.test --profile test_reftaxcustom"
-          - "tests/pipeline/misc/doubleprimers.nf.test --profile test_doubleprimers"
-          - "tests/pipeline/misc/fasta_input.nf.test --profile test_fasta"
-          - "tests/pipeline/misc/multi_seq.nf.test --profile test_multi"
-          - "tests/pipeline/paired_end/paired_end.nf.test --profile test"
-          - "tests/pipeline/paired_end/pe_iontorrent.nf.test --profile test_iontorrent"
-          - "tests/pipeline/paired_end/pe_novaseq.nf.test --profile test_novaseq"
-          - "tests/pipeline/paired_end/pe_pacbio_its.nf.test --profile test_pacbio_its"
-          - "tests/pipeline/single_end/single_end.nf.test --profile test_single"
+        tags:
+          - "test"
+          - "test_single"
+          - "test_fasta"
+          - "test_multi"
+          - "test_reftaxcustom"
+          - "test_doubleprimers"
+          - "test_iontorrent"
+          - "test_novaseq"
+          - "test_pacbio_its"
+          - "test_sintax"
+          - "test_pplace"
         profile:
           - "docker"
 
@@ -101,7 +103,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test ${{ matrix.component }},${{ matrix.profile }} --junitxml=test.xml
+          nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#580](https://github.com/nf-core/ampliseq/pull/580) - Add NF-TEST pipeline end-to-end tests for existing CI tests
 - [#591](https://github.com/nf-core/ampliseq/pull/591) - New version of the Unite taxonomy databases: 9.0
 - [#564](https://github.com/nf-core/ampliseq/pull/564),[#567](https://github.com/nf-core/ampliseq/pull/567),[#582](https://github.com/nf-core/ampliseq/pull/582) - Added phylogenetic placement
 - [#577](https://github.com/nf-core/ampliseq/pull/577) - Added SINTAX for taxonomic classification
@@ -15,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#580](https://github.com/nf-core/ampliseq/pull/580) - GitHub Actions CI - pull_request to `dev` tests with NXF_VER `latest-everything` & pull_request to `master` tests with NXF_VER `22.10.1` & `latest-everything`
 - [#563](https://github.com/nf-core/ampliseq/pull/563) - Renamed DADA2 taxonomic classification files to include the chosen reference taxonomy abbreviation.
 - [#567](https://github.com/nf-core/ampliseq/pull/567) - Renamed `--dada_tax_agglom_min` and `--qiime_tax_agglom_min` to `--tax_agglom_min` and `--dada_tax_agglom_max` and `--qiime_tax_agglom_max` to `--tax_agglom_max`
 - [#598](https://github.com/nf-core/ampliseq/pull/598) - Updated Workflow figure with SINTAX and phylogenetic placement

tests/pipeline/pplace.nf.test

@@ -0,0 +1,62 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_pplace"
+    tag "pipeline"
+
+    test("Pplace") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/overall_summary.tsv")).match("overall_summary_tsv") },
+                { assert snapshot(path("$outputDir/barrnap/rrna.arc.gff"),
+                                path("$outputDir/barrnap/rrna.bac.gff"),
+                                path("$outputDir/barrnap/rrna.euk.gff"),
+                                path("$outputDir/barrnap/rrna.mito.gff")).match("barrnap") },
+                { assert new File("$outputDir/barrnap/summary.tsv").exists() },
+                { assert snapshot(path("$outputDir/cutadapt/cutadapt_summary.tsv")).match("cutadapt") },
+                { assert snapshot(path("$outputDir/dada2/ASV_seqs.fasta"),
+                                path("$outputDir/dada2/ASV_table.tsv"),
+                                path("$outputDir/dada2/DADA2_stats.tsv"),
+                                path("$outputDir/dada2/DADA2_table.rds"),
+                                path("$outputDir/dada2/DADA2_table.tsv")).match("dada2") },
+                { assert snapshot(path("$outputDir/input/Samplesheet.tsv"),
+                                path("$outputDir/input/Metadata.tsv")).match("input") },
+                { assert new File("$outputDir/qiime2/abundance_tables/abs-abund-table-1.tsv").exists() },
+                { assert new File("$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/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("$outputDir/qiime2/rel_abundance_tables/rel-table-1.tsv").exists() },
+                { assert new File("$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-ASV.tsv").exists() },
+                { assert new File("$outputDir/qiime2/rel_abundance_tables/rel-table-ASV_with-PPLACE-tax.tsv").exists() },
+                { assert new File("$outputDir/qiime2/rel_abundance_tables/rel-table-ASV_with-QIIME2-tax.tsv").exists() },
+                { assert new File("$outputDir/qiime2/representative_sequences/filtered-sequences.qza").exists() },
+                { assert new File("$outputDir/qiime2/representative_sequences/rep-seq.fasta").exists() },
+                { assert snapshot(path("$outputDir/qiime2/representative_sequences/descriptive_stats.tsv"),
+                                path("$outputDir/qiime2/representative_sequences/seven_number_summary.tsv")).match("qiime2") },
+                { assert new File("$outputDir/pplace/test_pplace.taxonomy.per_query_unique.tsv").exists() },
+                { assert new File("$outputDir/pplace/test_pplace.taxonomy.per_query.tsv").exists() },
+                { assert new File("$outputDir/pplace/test_pplace.graft.test_pplace.epa_result.newick").exists() },
+                { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
+                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") }
+            )
+        }
+    }
+}

tests/pipeline/sintax.nf.test

@@ -0,0 +1,72 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_sintax"
+    tag "pipeline"
+
+    test("Sintax") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/overall_summary.tsv")).match("overall_summary_tsv") },
+                { assert snapshot(path("$outputDir/barrnap/rrna.arc.gff"),
+                                path("$outputDir/barrnap/rrna.bac.gff"),
+                                path("$outputDir/barrnap/rrna.euk.gff"),
+                                path("$outputDir/barrnap/rrna.mito.gff")).match("barrnap") },
+                { assert new File("$outputDir/barrnap/summary.tsv").exists() },
+                { assert snapshot(path("$outputDir/cutadapt/cutadapt_summary.tsv")).match("cutadapt") },
+                { assert snapshot(path("$outputDir/dada2/ASV_seqs.fasta"),
+                                path("$outputDir/dada2/ASV_table.tsv"),
+                                path("$outputDir/dada2/DADA2_stats.tsv"),
+                                path("$outputDir/dada2/DADA2_table.rds"),
+                                path("$outputDir/dada2/DADA2_table.tsv")).match("dada2") },
+                { 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("$outputDir/qiime2/rel_abundance_tables/rel-table-ASV_with-SINTAX-tax.tsv").exists() },
+                { assert new File("$outputDir/qiime2/representative_sequences/filtered-sequences.qza").exists() },
+                { assert new File("$outputDir/qiime2/representative_sequences/rep-seq.fasta").exists() },
+                { assert new File("$outputDir/qiime2/ancom/Category-var2-ASV/percent-abundances.tsv").exists() },
+                { assert new File("$outputDir/qiime2/ancom/Category-var3-ASV/percent-abundances.tsv").exists() },
+                { assert snapshot(path("$outputDir/qiime2/representative_sequences/descriptive_stats.tsv"),
+                                path("$outputDir/qiime2/representative_sequences/seven_number_summary.tsv")).match("qiime2") },
+                { assert snapshot(path("$outputDir/input/Samplesheet_pacbio_ITS.tsv"),
+                                path("$outputDir/input/Metadata_pacbio_ITS.tsv")).match("input") },
+                { assert new File("$outputDir/itsx/ASV_ITS_seqs.full.fasta").exists() },
+                { assert new File("$outputDir/itsx/ASV_ITS_seqs.ITS2.fasta").exists() },
+                { assert new File("$outputDir/itsx/ASV_ITS_seqs.summary.txt").exists() },
+                { assert new File("$outputDir/itsx/ITSx.args.txt").exists() },
+                { assert snapshot(path("$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("$outputDir/sintax/ASV_ITS_tax_sintax.unite-fungi.raw.tsv").exists() },
+                { assert new File("$outputDir/sintax/ASV_tax_sintax.unite-fungi.tsv").exists() },
+                { assert new File("$outputDir/sintax/ref_taxonomy_sintax.txt").exists() },
+                { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
+                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") }
+            )
+        }
+    }
+}