Add more nf tests

tests/.nftignore

@@ -6,26 +6,6 @@ multiqc/multiqc_data/multiqc_data.json
 multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_data/multiqc_software_versions.txt
 multiqc/multiqc_data/*.txt
-multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
 fastqc/*_fastqc.{html,zip}
 fastqc/*/*fastqc.zip
-pipeline_info/*.{html,json,txt,yml}
-bbduk/*.log
-nonpareil/*.{npa,npc,npl,npo,png,json,png,tsv,txt,pdf,csv}
-bracken/*combined_reports.txt
-centrifuge/*/*.mapped.fastq.gz
-centrifuge/*/*results.txt
-centrifuge/*/*.unmapped.fastq.gz
-diamond/*/*.{tsv,log,txt}
-fastp/*.{html,zip,json,log}
-kaiju/*/*.tsv
-kaiju/*.txt
-krona/*.html
-ganon/*/*.log
-kraken2/*/*.fastq.gz
-metaphlan/*/*.{biom,txt}
-porechop_abi/*.log
-samtools/*.bam.bai
-samtools/*.unmapped.bam
-taxpasta/*.tsv

tests/default.nf.test

@@ -15,22 +15,121 @@ 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_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name_all = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-           // def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            def stable_path     = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+
+             //MultiQC
+            def stable_name_multiqc      = getAllFilesFromDir("$outputDir/multiqc", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+	         //BBDuk
+            def stable_content_bbduk     = getAllFilesFromDir("$outputDir/bbduk", relative: true, includeDir: false, ignore: ['*.log'], ignoreFile: null, include: ['*','**/*'])
+            def stable_name_bbduk        = getAllFilesFromDir("$outputDir/bbduk", relative: true, includeDir: false, ignore: null , ignoreFile: null, include: ['**/*.fastq.gz'] )
+
+	          //DIAMOND
+            def stable_content_diamond   = getAllFilesFromDir("$outputDir/diamond", relative: true, includeDir: false, ignore: ['*/*.{tsv,log,txt}'], ignoreFile: null, include: ['*','**/*'])
+            def stable_name_diamond      = getAllFilesFromDir("$outputDir/diamond", relative: true, includeDir: false, ignore: null , ignoreFile: null, include: ['**/*.{tsv,log,txt}'] )
+
+            //nonpareil
+            def stable_content_nonpareil = getAllFilesFromDir("$outputDir/nonpareil", relative: true, includeDir: false, ignore: ['*.{svg,npa}'] , ignoreFile: null, include: ['*','**/*'])
+            def stable_name_nonpareil    = getAllFilesFromDir("$outputDir/nonpareil", relative: true, includeDir: false, ignore: null , ignoreFile: null, include: ['**/*.{svg,npa}'] )
+
+            //kraken2
+            def stable_content_kraken2   = getAllFilesFromDir("$outputDir/kraken2", relative: true, includeDir: false, ignore: ['**/*.fastq.gz'] , ignoreFile: null, include: ['*','**/*'])
+            def stable_name_kraken2      = getAllFilesFromDir("$outputDir/kraken2", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*.fastq.gz'])
+
+            //bowtie2
+            def stable_name_bowtie2      = getAllFilesFromDir("$outputDir/bowtie2", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+            //bracken
+            def stable_name_bracken      = getAllFilesFromDir("$outputDir/bracken", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+            //centrifuge
+            def stable_content_centrifuge   = getAllFilesFromDir("$outputDir/centrifuge", relative: true, includeDir: false, ignore: ['**/*.fastq.gz'] , ignoreFile: null, include: ['*','**/*'])
+            def stable_name_centrifuge   = getAllFilesFromDir("$outputDir/centrifuge", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+            //fastp
+            def stable_content_fastp     = getAllFilesFromDir("$outputDir/fastp", relative: true, includeDir: false, ignore: ['*.{log}'] , ignoreFile: null, include: ['*','**/*'])
+            def stable_name_fastp        = getAllFilesFromDir("$outputDir/fastp", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*.log'])
+
+            //ganon
+            def stable_name_ganon        = getAllFilesFromDir("$outputDir/ganon", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+            //kaiju
+            def stable_content_kaiju     = getAllFilesFromDir("$outputDir/kaiju", relative: true, includeDir: false, ignore: ['*.{tsv}'] , ignoreFile: null, include: ['*','**/*'])
+            def stable_name_kaiju        = getAllFilesFromDir("$outputDir/kaiju", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*.tsv'])
+
+            //kmcp
+            def stable_name_kmcp         = getAllFilesFromDir("$outputDir/kmcp", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+            // krona
+            def stable_name_krona        = getAllFilesFromDir("$outputDir/krona", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+            // metaphlan
+            def stable_name_metaphlan    = getAllFilesFromDir("$outputDir/metaphlan", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+            // nanoq
+            def stable_name_nanoq        = getAllFilesFromDir("$outputDir/nanoq", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+            // porechop_abi
+            def stable_content_porechopabi = getAllFilesFromDir("$outputDir/porechop_abi", relative: true, includeDir: false, ignore: ['*.{log}'] , ignoreFile: null, include: ['*','**/*'])
+            def stable_name_porechopabi  = getAllFilesFromDir("$outputDir/porechop_abi", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*.log'])
+
+            // samtools
+            def stable_name_samtools     = getAllFilesFromDir("$outputDir/samtools", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+            //taxpasta
+            def stable_name_taxpasta     = getAllFilesFromDir("$outputDir/taxpasta", relative: true, includeDir: false, ignore: null, ignoreFile: null, include: ['*', '**/*'])
+
+
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
                     // Number of successful tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_taxprofiler_software_mqc_versions.yml"),
-                    // All stable path name, with a relative path
-                   // stable_name,
-                    // All files with stable contents
-                    //stable_path
-                ).match() }
+                ).match() },
+
+                { assert new File("$outputDir/pipeline_info/nf_core_taxprofiler_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
+
+                { assert snapshot ( stable_name_all ).match("all_files") },
+		            { assert snapshot ( stable_name_multiqc ).match("multiqc" ) },
+                { assert snapshot( file("$outputDir/bbduk/2613_ERR5766181.bbduk.log").text.contains("Reads Processed:"), [stable_content_bbduk, stable_name_bbduk]).match("bbduk")},
+                { assert snapshot ( stable_content_diamond, stable_name_diamond ).match("diamond" ) },
+                { assert snapshot ( stable_content_nonpareil, stable_name_nonpareil ).match("nonpareil" ) },
+                  { assert snapshot (
+                        stable_name_kraken2, stable_content_kraken2, file ("$outputDir/kraken2/db2/2613_db2.kraken2.kraken2.report.txt").text.contains("S288C"), file ("$outputDir/kraken2/db2/2611_db2.kraken2.kraken2.report.txt").text.contains("S288C"), file ("$outputDir/kraken2/db2/2612_db2.kraken2.kraken2.report.txt").text.contains("S288C"))
+                        .match("kraken2") },
+                { assert snapshot ( stable_name_bowtie2, file ("$outputDir/bowtie2/align/2613_ERR5766181.bowtie2.log").text.contains("overall alignment rate"), file ("$outputDir/bowtie2/align/2612_ERR5766176_B.bowtie2.log").text.contains("overall alignment rate"), file ("$outputDir/bowtie2/align/2612_ERR5766176.bowtie2.log").text.contains("overall alignment rate"), file ("$outputDir/bowtie2/align/2612_ERR5766180.bowtie2.log").text.contains("overall alignment rate"),
+                        path("$outputDir/bowtie2/align/"))
+                        .match("bowtie2" ) },
+                { assert snapshot ( stable_name_bracken, file ("$outputDir/bracken/db1/2613_db1.bracken.tsv").text.contains("Homo sapiens"), file ("$outputDir/bracken/db1/2611_db1.bracken.tsv").text.contains("Homo sapiens"), file ("$outputDir/bracken/db1/2612_db1.bracken.tsv").text.contains("Homo sapiens"),
+                        path("$outputDir/bracken/db1"))
+                        .match("bracken") },
+                { assert snapshot ( stable_name_centrifuge, file ("$outputDir/centrifuge/db3/2613_db3.centrifuge.report.txt").text.contains("Eucommia"), file ("$outputDir/centrifuge/db3/2612_db3.centrifuge.report.txt").text.contains("Eucommia"),
+                        stable_content_centrifuge)
+                        .match("centrifuge") },
+                { assert snapshot ( file ("$outputDir/fastp/2613_ERR5766181.fastp.log").text.contains("Read pairs merged"),file ("$outputDir/fastp/2612_ERR5766176_B.fastp.log").text.contains("Read pairs merged"),file ("$outputDir/fastp/2612_ERR5766180.fastp.log").text.contains("Read pairs merged"),stable_content_fastp, stable_name_fastp ).match("fastp") },
+                { assert snapshot ( stable_name_ganon, file ("$outputDir/ganon/db1/2613_db1.ganon.tre").text.contains("Saccharomycetales"),file ("$outputDir/ganon/db1/2612_db1.ganon.tre").text.contains("Saccharomycetales"), file ("$outputDir/ganon/db1/2611_db1.ganon.tre").text.contains("Saccharomycetales"),
+                        path("$outputDir/ganon/db1"))
+                        .match("ganon") },
+                { assert snapshot ( file ("$outputDir/kaiju/db6/2614_db6.kaiju.tsv").text.contains("ERR3201952.3225565"),file ("$outputDir/kaiju/db6/ERR3201952_db6.kaiju.tsv").text.contains("ERR3201952.1159044"),stable_content_kaiju, stable_name_kaiju ).match("kaiju") },
+                { assert snapshot ( stable_name_kmcp, file ("$outputDir/kmcp/db1/2613_db1.kmcp.profile").text.contains("NW_024067565.1"),file ("$outputDir/kmcp/db1/2612_db1.kmcp.profile").text.contains("NW_024067565.1"),file ("$outputDir/kmcp/db1/2611_db1.kmcp.profile").text.contains("NW_024067565.1"),
+                        path("$outputDir/kmcp/db1"))
+                        .match("kmcp") },
+                { assert snapshot ( stable_name_krona, path("$outputDir/krona")).match("krona" ) },
+                { assert snapshot ( stable_name_metaphlan, file ("$outputDir/metaphlan/metaphlan4/2613_metaphlan4.metaphlan_profile.txt").text.contains("SGB4933_group")).match("metaphlan") },
+                { assert snapshot(path("$outputDir/metaphlan/metaphlan4/2613_metaphlan4.metaphlan_profile.txt").md5).match("metaphlan_profile_md5") },
+                { assert snapshot ( stable_name_nanoq, file ("$outputDir/nanoq/ERR3201952_ERR3201952_filtered.stats").text.contains("Median read quality")).match("nanoq") },
+                { assert snapshot(path("$outputDir/nanoq/ERR3201952_ERR3201952_filtered.stats").md5).match("nanoq_md5") },
+                { assert snapshot ( file ("$outputDir/porechop_abi/ERR3201952_ERR3201952_porechop_abi.log").text.contains("reads were split"), [stable_name_porechopabi, stable_content_porechopabi]).match("porechop_abi") },
+                { assert snapshot ( stable_name_samtools, file ("$outputDir/samtools/stats/2613_ERR5766181.stats").text.contains("mismatches:")).match("samtools") },
+                { assert snapshot(path("$outputDir/samtools/stats/2613_ERR5766181.stats").md5).match("samtools_md5") },
+                { assert snapshot ( stable_name_taxpasta, file ("$outputDir/taxpasta/metaphlan_metaphlan4.tsv").text.contains("186803")).match("taxpasta") },
+                { assert snapshot(path("$outputDir/taxpasta/metaphlan_metaphlan4.tsv").md5).match("taxpasta_md5") },
             )
         }
     }