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Add new test_alternatives process - missing some processes #834

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1 change: 1 addition & 0 deletions conf/test.config
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Expand Up @@ -3,6 +3,7 @@
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.
Runs all default tools, with a couple of 'would most likely run anyway' options.

Use as follows:
nextflow run nf-core/mag -profile test,<docker/singularity> --outdir <OUTDIR>
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50 changes: 50 additions & 0 deletions conf/test_alternatives.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.
Includes all third mutually exclusive options, and performs coassembly

Use as follows:
nextflow run nf-core/mag -profile test_alternatives,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '1.h',
]
}

params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
input = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.multirun.v4.csv'

clip_tool = 'trimmomatic'

min_length_unbinned_contigs = 1
max_unbinned_contigs = 2

coassemble_group = true

// Including (even length filtered) CONOCT bins adds another 5 minutes, so we skip it in the default test (testing in assemblyinput)
skip_concoct = true

binqc_tool = 'checkm2'
bin_domain_classification = true

// Prokka is the slowest step of the tests, so we speed up by turning off CDS/product searching
prokka_fast_mode = true
gtdb_db = params.pipelines_testdata_base_path + 'mag/databases/gtdbtk/gtdbtk_mockup_20250422.tar.gz'
cat_db = params.pipelines_testdata_base_path + 'mag/databases/cat/minigut_cat.tar.gz'
cat_no_suggestive_asterisks = true
gtdbtk_min_completeness = 0.01
// Required for the small GTDBTk dummy database aa
gtdbtk_use_full_tree = true
}
3 changes: 2 additions & 1 deletion conf/test_single_end.config
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Expand Up @@ -3,6 +3,8 @@
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.
Runs with single-end input, with second mutually exclusive options,
and runs the ancient DNA mode.

Use as follows:
nextflow run nf-core/mag -profile test_single_end,<docker/singularity> --outdir <OUTDIR>
Expand Down Expand Up @@ -33,7 +35,6 @@ params {
spades_fix_cpus = 1
binning_map_mode = 'own'
ancient_dna = true
binning_map_mode = 'own'
skip_spades = false
skip_spadeshybrid = true
bcftools_view_high_variant_quality = 0
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3 changes: 3 additions & 0 deletions nextflow.config
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Expand Up @@ -370,6 +370,9 @@ profiles {
test_longread {
includeConfig 'conf/test_longread.config'
}
test_alternatives {
includeConfig 'conf/test_alternatives.config'
}
}

// Load nf-core custom profiles from different institutions
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37 changes: 37 additions & 0 deletions tests/test_alternatives.nf.test
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nextflow_pipeline {

name "Test pipeline"
script "../main.nf"
tag "pipeline"
tag "test_alternatives"
profile "test_alternatives"

test("-profile test_single_end") {

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, ignore: ['pipeline_info/*.{html,json,txt}'])
// // stable_path: All files in ${params.outdir}/ with stable content
// def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
assertAll(
{ assert workflow.success},
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_mag_software_mqc_versions.yml"),
// // All stable path name, with a relative path
// stable_name,
// // All files with stable contents
// stable_path
).match() }
)
}
}
}
126 changes: 126 additions & 0 deletions tests/test_alternatives.nf.test.snap
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{
"-profile test_single_end": {
"content": [
130,
{
"BOWTIE2_ASSEMBLY_ALIGN": {
"bowtie2": "2.4.2",
"samtools": 1.11,
"pigz": "2.3.4"
},
"BOWTIE2_PHIX_REMOVAL_ALIGN": {
"bowtie2": "2.4.2"
},
"CATPACK_ADDNAMES_BINS": {
"catpack": 6.0
},
"CATPACK_BINS": {
"catpack": 6.0
},
"CATPACK_SUMMARISE_BINS": {
"catpack": 6.0
},
"CAT_FASTQ": {
"cat": 9.5
},
"CHECKM2_PREDICT": {
"checkm2": "1.1.0"
},
"CONCAT_BINQC_TSV": {
"csvtk": "0.31.0"
},
"CONVERT_DEPTHS": {
"bioawk": 20110810
},
"DASTOOL_FASTATOCONTIG2BIN_TIARA": {
"dastool": "1.1.6"
},
"FASTQC_RAW": {
"fastqc": "0.12.1"
},
"FASTQC_TRIMMED": {
"fastqc": "0.12.1"
},
"GTDBTK_CLASSIFYWF": {
"gtdbtk": "2.4.0"
},
"GUNZIP_BINS": {
"gunzip": 1.13
},
"GUNZIP_SHORTREAD_ASSEMBLIES": {
"gunzip": 1.13
},
"GUNZIP_UNBINS": {
"gunzip": 1.13
},
"MAG_DEPTHS": {
"python": "3.6.7",
"pandas": "1.1.5"
},
"MAG_DEPTHS_PLOT": {
"python": "3.9.6",
"pandas": "1.3.0",
"seaborn": "0.11.0"
},
"MAG_DEPTHS_SUMMARY": {
"python": "3.10.6",
"pandas": "1.4.3"
},
"MAXBIN2": {
"maxbin2": "2.2.7"
},
"MEGAHIT": {
"megahit": "1.2.9"
},
"METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD": {
"metabat2": 2.15
},
"METABAT2_METABAT2": {
"metabat2": 2.15
},
"METASPADES": {
"spades": "4.1.0"
},
"POOL_PAIRED_READS": {
"cat": 8.3
},
"PRODIGAL": {
"prodigal": "2.6.3",
"pigz": 2.6
},
"PROKKA": {
"prokka": "1.14.6"
},
"QUAST": {
"python": "3.7.6",
"metaquast": "5.0.2"
},
"QUAST_BINS": {
"python": "3.7.6",
"metaquast": "5.0.2"
},
"SPLIT_FASTA": {
"python": "3.6.7",
"biopython": "1.7.4",
"pandas": "1.1.5"
},
"TIARA_TIARA": {
"tiara": "1.0.3"
},
"TRIMMOMATIC": {
"trimmomatic": 0.39
},
"Workflow": {
"nf-core/mag": "v4.1.0dev"
},
"r-base": "4.1.3",
"r-tidyverse": "1.3.1"
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.4"
},
"timestamp": "2025-06-22T05:43:48.636211777"
}
}
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