Snapshot for -profile test_assembly_input

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#905](https://github.com/nf-core/mag/pull/905) - Add nf-test snapshot for `test_assembly_input` profile (by @dialvarezs)
+
 ### `Changed`
 
 ### `Fixed`

conf/test_assembly_input.config

@@ -22,6 +22,7 @@ process {
 
 process {
     withName: METAEUK_EASYPREDICT {
+        cpus = 1  // to keep output order consistent
         ext.args = '-s 1 --max-seqs 10 --max-accept 1'
     }
 }
@@ -36,6 +37,7 @@ params {
 
     busco_db                        = params.pipelines_testdata_base_path + 'mag/databases/busco/bacteria_odb10.2024-01-08.tar.gz'
     busco_db_lineage                = 'bacteria_odb10'
+    busco_clean                     = true
 
     skip_quast                      = true
     skip_prodigal                   = true

modules/local/tiara_classify/main.nf

@@ -42,6 +42,7 @@ process TIARA_CLASSIFY {
     done < bin2classification.tsv
 
     cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
         r-base: \$(R --version | head -n 1 | grep -Eo '[0-9.]+ ')
         r-tidyverse: \$(cat tidyverse_version.txt)
     END_VERSIONS

nf-test.config

@@ -19,7 +19,8 @@ config {
 
     // load the necessary plugins
     plugins {
-        load "nft-utils@0.0.3"
+        load "nft-csv@0.1.0"
         load "[email protected]"
+        load "[email protected]"
     }
 }

tests/.nftignore

@@ -1,27 +1,34 @@
 .DS_Store
-multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
-multiqc/multiqc_data/multiqc.parquet
-multiqc/multiqc_data/multiqc.log
-multiqc/multiqc_data/multiqc_data.json
-multiqc/multiqc_data/multiqc_sources.txt
-multiqc/multiqc_data/multiqc_sources.yaml
-multiqc/multiqc_data/multiqc_software_versions.txt
-multiqc/multiqc_data/multiqc_software_versions.yaml
-multiqc/multiqc_data/llms-full.txt
-multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
-multiqc/multiqc_report.html
-pipeline_info/*.{html,json,txt,yml}
 Assembly/MEGAHIT/*.log
 Assembly/MEGAHIT/QC/*/*.bowtie2.log
+GenomeBinning/CONCOCT/stats/*_{original,PCA_components,PCA_transformed}_data_gt1000.csv
+GenomeBinning/CONCOCT/stats/*_log.txt
+GenomeBinning/CONCOCT/stats/*.tsv
+GenomeBinning/DASTool/*.log
 GenomeBinning/depths/**/*-depth.txt.gz
 GenomeBinning/depths/bins/*.png
 GenomeBinning/MetaBAT2/unbinned/discarded/*.unbinned.pooled.fa.gz
-GenomeBinning/QC/CheckM2/**/DIAMOND_RESULTS.tsv
-GenomeBinning/QC/CheckM2/*/checkm2.log
 GenomeBinning/QC/busco_summary.tsv
-GenomeBinning/QC/BUSCO/**/*.log
 GenomeBinning/QC/BUSCO/**/.checkpoint
+GenomeBinning/QC/BUSCO/**/{logs,prodigal_output,busco_sequences}/**
 GenomeBinning/QC/BUSCO/**/*.json
+GenomeBinning/QC/BUSCO/**/*.log
 GenomeBinning/QC/BUSCO/**/*.txt
+GenomeBinning/QC/BUSCO/**/short_summary*.{txt,json}
+GenomeBinning/QC/BUSCO/*/*{-busco.log,-busco.batch_summary.txt}
+GenomeBinning/QC/CheckM2/**/DIAMOND_RESULTS.tsv
+GenomeBinning/QC/CheckM2/*/checkm2.log
+multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/multiqc_data/llms-full.txt
+multiqc/multiqc_data/multiqc_data.json
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_data/multiqc_software_versions.yaml
+multiqc/multiqc_data/multiqc_sources.txt
+multiqc/multiqc_data/multiqc_sources.yaml
+multiqc/multiqc_data/multiqc.log
+multiqc/multiqc_data/multiqc.parquet
+multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/multiqc_report.html
+pipeline_info/*.{html,json,txt,yml}
 QC_shortreads/fastqc/*_fastqc.{html,zip}
 QC_shortreads/remove_phix/*.log

tests/default.nf.test.snap

@@ -6,13 +6,13 @@
                     "coreutils": 9.5
                 },
                 "BIN_SUMMARY": {
-                    "python": "3.10.6",
-                    "pandas": "1.4.3"
+                    "pandas": "1.4.3",
+                    "python": "3.10.6"
                 },
                 "BOWTIE2_ASSEMBLY_ALIGN": {
                     "bowtie2": "2.4.2",
-                    "samtools": 1.11,
-                    "pigz": "2.3.4"
+                    "pigz": "2.3.4",
+                    "samtools": 1.11
                 },
                 "BOWTIE2_ASSEMBLY_BUILD": {
                     "bowtie2": "2.4.2"
@@ -60,15 +60,15 @@
                     "fastqc": "0.12.1"
                 },
                 "GTDBTK_CLASSIFYWF": {
-                    "gtdbtk": "2.5.2",
-                    "gtdb_db": "r226"
+                    "gtdb_db": "r226",
+                    "gtdbtk": "2.5.2"
                 },
                 "GTDBTK_DB_PREPARATION": {
                     "tar": 1.34
                 },
                 "GTDBTK_SUMMARY": {
-                    "python": "3.10.6",
-                    "pandas": "1.4.3"
+                    "pandas": "1.4.3",
+                    "python": "3.10.6"
                 },
                 "GUNZIP_BINS": {
                     "gunzip": 1.13
@@ -80,17 +80,17 @@
                     "gunzip": 1.13
                 },
                 "MAG_DEPTHS": {
-                    "python": "3.6.7",
-                    "pandas": "1.1.5"
+                    "pandas": "1.1.5",
+                    "python": "3.6.7"
                 },
                 "MAG_DEPTHS_PLOT": {
-                    "python": "3.9.6",
                     "pandas": "1.3.0",
+                    "python": "3.9.6",
                     "seaborn": "0.11.0"
                 },
                 "MAG_DEPTHS_SUMMARY": {
-                    "python": "3.10.6",
-                    "pandas": "1.4.3"
+                    "pandas": "1.4.3",
+                    "python": "3.10.6"
                 },
                 "MAXBIN2": {
                     "maxbin2": "2.2.7"
@@ -108,19 +108,19 @@
                     "spades": "4.1.0"
                 },
                 "PRODIGAL": {
-                    "prodigal": "2.6.3",
-                    "pigz": 2.6
+                    "pigz": 2.6,
+                    "prodigal": "2.6.3"
                 },
                 "PROKKA": {
                     "prokka": "1.14.6"
                 },
                 "QUAST": {
-                    "python": "3.7.6",
-                    "metaquast": "5.0.2"
+                    "metaquast": "5.0.2",
+                    "python": "3.7.6"
                 },
                 "QUAST_BINS": {
-                    "python": "3.7.6",
-                    "metaquast": "5.0.2"
+                    "metaquast": "5.0.2",
+                    "python": "3.7.6"
                 },
                 "QUAST_BINS_SUMMARY": {
                     "cp": 9.5
@@ -129,9 +129,9 @@
                     "seqkit": "2.9.0"
                 },
                 "SPLIT_FASTA": {
-                    "python": "3.6.7",
                     "biopython": "1.7.4",
-                    "pandas": "1.1.5"
+                    "pandas": "1.1.5",
+                    "python": "3.6.7"
                 },
                 "Workflow": {
                     "nf-core/mag": "v5.3.0dev"
@@ -142,7 +142,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:47:54.060594176"
+        "timestamp": "2025-11-11T08:17:18.125734263"
     },
     "multiqc": {
         "content": [

tests/test_alternatives.nf.test

@@ -10,7 +10,7 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "${outputDir}"
             }
         }
 
@@ -61,7 +61,7 @@ nextflow_pipeline {
                 params.outdir, include: ['GenomeBinning/MetaBAT2/bins/*.fa.gz']
             )
             def metabat2_unbins = getAllFilesFromDir(
-                params.outdir, include: ['GenomeBinning/MetaBAT2/{discarded,unbinned}/*.fa.gz']
+                params.outdir, include: ['GenomeBinning/MetaBAT2/{discarded,unbinned/*}/*.fa.gz']
             )
 
             // Output dir: multiqc
@@ -72,13 +72,12 @@ nextflow_pipeline {
                 params.outdir, include: ['multiqc/**'], ignoreFile: 'tests/.nftignore'
             )
 
+            assert workflow.success
             assertAll(
-                { assert workflow.success },
                 { assert snapshot(
-                        workflow.trace.succeeded().size(),
-                        removeNextflowVersion("${outputDir}/pipeline_info/nf_core_mag_software_mqc_versions.yml"),
-                    ).match()
-                },
+                    workflow.trace.succeeded().size(),
+                    removeNextflowVersion("${outputDir}/pipeline_info/nf_core_mag_software_mqc_versions.yml"),
+                ).match() },
                 { assert snapshot(stable_name_qc,       stable_path_qc      ).match('qc') },
                 { assert snapshot(stable_name_assembly, stable_path_assembly).match('assembly') },
                 { assert snapshot(stable_name_binning,  stable_path_binning ).match('binning') },
@@ -87,10 +86,12 @@ nextflow_pipeline {
                         checkm2_diamond_results.collect { results -> results.text.readLines().size() },
                     ).match('checkm2_diamond_results')
                 },
+
                 // FASTA checks
                 { assert megahit_contigs.collect { contigs -> path("${contigs}").fasta.size() > 0 }.every() },
                 { assert metabat2_bins.collect { contigs -> path("${contigs}").fasta.size() > 0 }.every() },
                 { assert metabat2_unbins.collect { contigs -> path("${contigs}").fasta.size() >= 0 }.every() },
+
                 // Log checks
                 { assert remove_phix_logs.collect {
                         log -> log.readLines().last() ==~ /[0-9.]+% overall alignment rate/

tests/test_alternatives.nf.test.snap

@@ -16,13 +16,13 @@
             43,
             {
                 "BIN_SUMMARY": {
-                    "python": "3.10.6",
-                    "pandas": "1.4.3"
+                    "pandas": "1.4.3",
+                    "python": "3.10.6"
                 },
                 "BOWTIE2_ASSEMBLY_ALIGN": {
                     "bowtie2": "2.4.2",
-                    "samtools": 1.11,
-                    "pigz": "2.3.4"
+                    "pigz": "2.3.4",
+                    "samtools": 1.11
                 },
                 "BOWTIE2_ASSEMBLY_BUILD": {
                     "bowtie2": "2.4.2"
@@ -64,17 +64,17 @@
                     "gunzip": 1.13
                 },
                 "MAG_DEPTHS": {
-                    "python": "3.6.7",
-                    "pandas": "1.1.5"
+                    "pandas": "1.1.5",
+                    "python": "3.6.7"
                 },
                 "MAG_DEPTHS_PLOT": {
-                    "python": "3.9.6",
                     "pandas": "1.3.0",
+                    "python": "3.9.6",
                     "seaborn": "0.11.0"
                 },
                 "MAG_DEPTHS_SUMMARY": {
-                    "python": "3.10.6",
-                    "pandas": "1.4.3"
+                    "pandas": "1.4.3",
+                    "python": "3.10.6"
                 },
                 "MEGAHIT": {
                     "megahit": "1.2.9"
@@ -89,9 +89,13 @@
                     "seqkit": "2.9.0"
                 },
                 "SPLIT_FASTA": {
-                    "python": "3.6.7",
                     "biopython": "1.7.4",
-                    "pandas": "1.1.5"
+                    "pandas": "1.1.5",
+                    "python": "3.6.7"
+                },
+                "TIARA_CLASSIFY": {
+                    "r-base": "4.1.3",
+                    "r-tidyverse": "1.3.1"
                 },
                 "TIARA_SUMMARY": {
                     "csvtk": "0.31.0"
@@ -104,16 +108,14 @@
                 },
                 "Workflow": {
                     "nf-core/mag": "v5.3.0dev"
-                },
-                "r-base": "4.1.3",
-                "r-tidyverse": "1.3.1"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:50:38.41461775"
+        "timestamp": "2025-11-12T08:15:35.162392538"
     },
     "qc": {
         "content": [
@@ -240,11 +242,7 @@
                 "MEGAHIT-MetaBAT2-test_minigut_sample2.tooShort.fa.gz:md5,f9479e7fb34586a2892cd7bc323d414a",
                 "MEGAHIT-MetaBAT2-test_minigut.unbinned.remaining.fa.gz:md5,7ac001a38113812061f8ef5c94e3f579",
                 "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.remaining.fa.gz:md5,e1a969d6e292e10a81ef4236907984a9",
-                "predicted.faa:md5,8e0d0014fb0a1e56fa8b8f47e20f2bcf",
-                "predicted.fna:md5,e4dc769d029b05cfe724cfa5ef214f10",
                 "refseq_db.faa:md5,0d53f0a1964cc202e99f4851839273a3",
-                "predicted.faa:md5,5e5160a0e0af28ccccd6459e887269ee",
-                "predicted.fna:md5,df236064ad2e0c699c029a89a6267bcf",
                 "refseq_db.faa:md5,0d53f0a1964cc202e99f4851839273a3",
                 "MEGAHIT-MetaBAT2-test_minigut.1.faa:md5,ba436cbba64ce111f228da1e2daac642",
                 "MEGAHIT-MetaBAT2-test_minigut.2.faa:md5,577adc1aa1ebd51fed46f726ad90d9b3",