Add more nf-tests

.github/workflows/nf-test.yml

@@ -57,7 +57,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 7
+          max_shards: 10
 
       - name: debug
         run: |

CHANGELOG.md

@@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#225](https://github.com/nf-core/bacass/pull/225) add BUSCO nf-core module.
 - [#223](https://github.com/nf-core/bacass/pull/223) Add nf-core/filtlong module.
 - [#222](https://github.com/nf-core/bacass/pull/222) Reinstalled Dragonflye 1.1.2.
-- [#195](https://github.com/nf-core/bacass/pull/195) Update nf-core/bacass to the new nf-core 3.2.0 `TEMPLATE`.
+- [#195](https://github.com/nf-core/bacass/pull/195),[#252](https://github.com/nf-core/bacass/pull/252) Update nf-core/bacass to the new nf-core 3.2.0 `TEMPLATE` and added nf-test
 
 ### `Fixed`
 

tests/.nftignore

@@ -6,25 +6,26 @@ multiqc/multiqc_data/multiqc_sources.{txt,yaml}
 multiqc/multiqc_data/multiqc_software_versions.{txt,yaml}
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
+multiqc/multiqc_data/mqc_prokka_plot_1.yaml
+multiqc/multiqc_data/multiqc_prokka.yaml
+multiqc/multiqc_data/multiqc_general_stats.yaml
+multiqc/multiqc_data/mqc_quast_num_contigs_1.yaml
+multiqc/multiqc_data/multiqc_quast.yaml
+multiqc/multiqc_data/porechop.yaml
 fastqc/*_fastqc.{html,zip}
 FastQC/raw/*.{html,zip}
-FastQC/trim/*.html,zip
+FastQC/trim/*.{html,zip}
 pipeline_info/*.{html,json,txt,yml}
-busco/*.batch_summary.txt
-busco/*.log
-busco/**/logs/hmmsearch_out.log
-busco/**/.checkpoint
-busco/**/hmmer_output/*.out
-busco/**/run_bacteria_odb10/short_summary.{txt,json}
-busco/*.batch_summary.txt
-busco/short_summary.specific.bacteria_odb10.*.scaffolds.fa.{json,txt}
+busco/**
+busco/*
 trimming/shortreads/json_html/*.fastp.html
 trimming/shortreads/log/*.fastp.log
+trimming/longreads/porechop/*.porechop.log
 Prokka/*/*.{gbk,sqn,log,err}
-QUAST/report/basic_stats/*.scaffolds_GC_content_plot.pdf
-QUAST/report/basic_stats/{GC_content_plot,Nx_plot,cumulative_plot}.pdf
-QUAST/report/quast.log
-QUAST/report/report.{html,pdf}
+QUAST/report/**
 Unicycler/*.unicycler.log
-.checkpoint
-**/.checkpoint
+DFAST/*/*.{tsv,log,gbk}
+QC_longreads/ToulligQC/**
+QC_longreads/NanoPlot/*
+Dragonflye/*
+Medaka/*

tests/.nftignore_files_entirely

@@ -0,0 +1,7 @@
+.DS_Store
+pipeline_info/*.{html,json,txt}
+busco/busco_downloads/**
+busco/**/busco_sequences/**
+busco/**/hmmer_output/**
+QC_longreads/ToulligQC/**
+QC_longreads/NanoPlot/*.log

tests/default.nf.test

@@ -3,6 +3,8 @@ nextflow_pipeline {
     name "Test pipeline"
     script "../main.nf"
     tag "pipeline"
+    profile "test"
+
     test("-profile test") {
 
         when {
@@ -13,7 +15,7 @@ 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}'])
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely')
             // stable_path: All files in ${params.outdir}/ with stable content
             def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(

tests/dfast.nf.test

@@ -0,0 +1,36 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    profile "test_dfast"
+
+    test("-profile test_dfast") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely')
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_bacass_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}