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Merge pull request #905 from dialvarezs/snapshot_assembly_input
Snapshot for `-profile test_assembly_input`
2 parents a9f0087 + c8f62e6 commit 5868522

14 files changed

+703
-144
lines changed

‎CHANGELOG.md‎

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

‎conf/test_assembly_input.config‎

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

‎modules/local/tiara_classify/main.nf‎

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

‎nf-test.config‎

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

‎tests/.nftignore‎

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

‎tests/default.nf.test.snap‎

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

‎tests/test_alternatives.nf.test‎

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@@ -10,7 +10,7 @@ nextflow_pipeline {
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when {
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params {
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outdir = "$outputDir"
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outdir = "${outputDir}"
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}
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}
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params.outdir, include: ['GenomeBinning/MetaBAT2/bins/*.fa.gz']
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)
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def metabat2_unbins = getAllFilesFromDir(
64-
params.outdir, include: ['GenomeBinning/MetaBAT2/{discarded,unbinned}/*.fa.gz']
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params.outdir, include: ['GenomeBinning/MetaBAT2/{discarded,unbinned/*}/*.fa.gz']
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)
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// Output dir: multiqc
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params.outdir, include: ['multiqc/**'], ignoreFile: 'tests/.nftignore'
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)
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assert workflow.success
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assertAll(
76-
{ assert workflow.success },
7777
{ assert snapshot(
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workflow.trace.succeeded().size(),
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removeNextflowVersion("${outputDir}/pipeline_info/nf_core_mag_software_mqc_versions.yml"),
80-
).match()
81-
},
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workflow.trace.succeeded().size(),
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removeNextflowVersion("${outputDir}/pipeline_info/nf_core_mag_software_mqc_versions.yml"),
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).match() },
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{ assert snapshot(stable_name_qc, stable_path_qc ).match('qc') },
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{ assert snapshot(stable_name_assembly, stable_path_assembly).match('assembly') },
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{ assert snapshot(stable_name_binning, stable_path_binning ).match('binning') },
@@ -87,10 +86,12 @@ nextflow_pipeline {
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checkm2_diamond_results.collect { results -> results.text.readLines().size() },
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).match('checkm2_diamond_results')
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},
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// FASTA checks
9191
{ assert megahit_contigs.collect { contigs -> path("${contigs}").fasta.size() > 0 }.every() },
9292
{ assert metabat2_bins.collect { contigs -> path("${contigs}").fasta.size() > 0 }.every() },
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{ assert metabat2_unbins.collect { contigs -> path("${contigs}").fasta.size() >= 0 }.every() },
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// Log checks
9596
{ assert remove_phix_logs.collect {
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log -> log.readLines().last() ==~ /[0-9.]+% overall alignment rate/

‎tests/test_alternatives.nf.test.snap‎

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{
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"BIN_SUMMARY": {
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"python": "3.10.6",
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"pandas": "1.4.3"
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"pandas": "1.4.3",
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"python": "3.10.6"
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},
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"BOWTIE2_ASSEMBLY_ALIGN": {
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"bowtie2": "2.4.2",
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"samtools": 1.11,
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"pigz": "2.3.4"
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"pigz": "2.3.4",
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"samtools": 1.11
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},
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"BOWTIE2_ASSEMBLY_BUILD": {
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"bowtie2": "2.4.2"
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"gunzip": 1.13
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},
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"MAG_DEPTHS": {
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"python": "3.6.7",
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"pandas": "1.1.5"
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"pandas": "1.1.5",
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"python": "3.6.7"
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},
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"MAG_DEPTHS_PLOT": {
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"python": "3.9.6",
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"pandas": "1.3.0",
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"python": "3.9.6",
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"seaborn": "0.11.0"
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},
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"MAG_DEPTHS_SUMMARY": {
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"python": "3.10.6",
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"pandas": "1.4.3"
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"pandas": "1.4.3",
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"python": "3.10.6"
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},
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"MEGAHIT": {
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"megahit": "1.2.9"
@@ -89,9 +89,13 @@
8989
"seqkit": "2.9.0"
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},
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"SPLIT_FASTA": {
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"python": "3.6.7",
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"biopython": "1.7.4",
94-
"pandas": "1.1.5"
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"pandas": "1.1.5",
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"python": "3.6.7"
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},
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"TIARA_CLASSIFY": {
97+
"r-base": "4.1.3",
98+
"r-tidyverse": "1.3.1"
9599
},
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"TIARA_SUMMARY": {
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"csvtk": "0.31.0"
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},
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"Workflow": {
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"nf-core/mag": "v5.3.0dev"
107-
},
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"r-base": "4.1.3",
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"r-tidyverse": "1.3.1"
111+
}
110112
}
111113
],
112114
"meta": {
113115
"nf-test": "0.9.3",
114116
"nextflow": "25.10.0"
115117
},
116-
"timestamp": "2025-11-07T11:50:38.41461775"
118+
"timestamp": "2025-11-12T08:15:35.162392538"
117119
},
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"qc": {
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"content": [
@@ -240,11 +242,7 @@
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"MEGAHIT-MetaBAT2-test_minigut_sample2.tooShort.fa.gz:md5,f9479e7fb34586a2892cd7bc323d414a",
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"MEGAHIT-MetaBAT2-test_minigut.unbinned.remaining.fa.gz:md5,7ac001a38113812061f8ef5c94e3f579",
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"MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.remaining.fa.gz:md5,e1a969d6e292e10a81ef4236907984a9",
243-
"predicted.faa:md5,8e0d0014fb0a1e56fa8b8f47e20f2bcf",
244-
"predicted.fna:md5,e4dc769d029b05cfe724cfa5ef214f10",
245245
"refseq_db.faa:md5,0d53f0a1964cc202e99f4851839273a3",
246-
"predicted.faa:md5,5e5160a0e0af28ccccd6459e887269ee",
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"predicted.fna:md5,df236064ad2e0c699c029a89a6267bcf",
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"refseq_db.faa:md5,0d53f0a1964cc202e99f4851839273a3",
249247
"MEGAHIT-MetaBAT2-test_minigut.1.faa:md5,ba436cbba64ce111f228da1e2daac642",
250248
"MEGAHIT-MetaBAT2-test_minigut.2.faa:md5,577adc1aa1ebd51fed46f726ad90d9b3",

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