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Merge pull request #57 from nf-core/malt-faa-support
Add MALT amino acid support
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Nextflow config file for running minimal tests | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Defines input files and everything required to run a fast and simple pipeline test. | ||
| Use as follows: | ||
| nextflow run nf-core/createtaxdb -profile test_alternatives,<docker/singularity> --outdir <OUTDIR> | ||
| This config is for testing mutually exclusive options to those in the default `test` | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| process { | ||
| resourceLimits = [ | ||
| cpus: 4, | ||
| memory: '15.GB', | ||
| time: '1.h', | ||
| ] | ||
| } | ||
|
|
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| params { | ||
| config_profile_name = 'Test profile' | ||
| config_profile_description = 'Minimal test dataset to check pipeline function' | ||
|
|
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| // Input data | ||
| input = params.pipelines_testdata_base_path + 'createtaxdb/samplesheets/test.csv' | ||
|
|
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| dbname = "database" | ||
|
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| build_bracken = false | ||
| build_diamond = false | ||
| build_ganon = false | ||
| build_kaiju = false | ||
| build_malt = true | ||
| build_centrifuge = false | ||
| build_kraken2 = false | ||
| build_krakenuniq = false | ||
|
|
||
| krakenuniq_build_params = "--work-on-disk --max-db-size 14 --kmer-len 15 --minimizer-len 13 --jellyfish-bin \"\$(which jellyfish)\"" | ||
| malt_build_params = "--sequenceType Protein" | ||
|
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| accession2taxid = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/nucl_gb.accession2taxid' | ||
| nucl2taxid = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/nucl2tax.map' | ||
| prot2taxid = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/prot.accession2taxid.gz' | ||
| nodesdmp = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/nodes.dmp' | ||
| namesdmp = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/names.dmp' | ||
| malt_mapdb = 's3://ngi-igenomes/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip' | ||
| } | ||
|
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||
| process { | ||
| withName: KRAKENUNIQ_BUILD { | ||
| memory = { 12.GB * task.attempt } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| nextflow_pipeline { | ||
|
|
||
| name "Test pipeline: NFCORE_CREATETAXDB" | ||
| script "main.nf" | ||
| tag "pipeline" | ||
| tag "nfcore_createtaxdb" | ||
| tag "test_alternatives" | ||
|
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| test("test_alternatives_profile") { | ||
|
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| when { | ||
| params { | ||
| outdir = "$outputDir" | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot( | ||
| path("$outputDir/malt/malt-build.log").readLines().last().contains('Peak memory'), | ||
| path("$outputDir/malt/malt_index/index0.idx"), | ||
| path("$outputDir/malt/malt_index/ref.db"), | ||
| path("$outputDir/malt/malt_index/ref.idx"), | ||
| path("$outputDir/malt/malt_index/ref.inf"), | ||
| path("$outputDir/malt/malt_index/taxonomy.idx"), | ||
| path("$outputDir/malt/malt_index/taxonomy.map"), | ||
| path("$outputDir/malt/malt_index/taxonomy.tre") | ||
| ).match() | ||
| }, | ||
| { assert new File("$outputDir/pipeline_info/nf_core_createtaxdb_software_mqc_versions.yml").exists() }, | ||
| { assert new File("$outputDir/multiqc/multiqc_report.html").exists() }, | ||
| { assert path("$outputDir/malt/malt_index/table0.db").exists() }, | ||
| { assert path("$outputDir/malt/malt_index/table0.idx").exists() }, | ||
| ) | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| { | ||
| "test_alternatives_profile": { | ||
| "content": [ | ||
| true, | ||
| "index0.idx:md5,ef349ebc456d6446b75570b8a0e57c0d", | ||
| "ref.db:md5,9372b49e5990fb4b29ed986a1fc737c4", | ||
| "ref.idx:md5,b99c3dc612948a7e4e490c3c74498c80", | ||
| "ref.inf:md5,e7ae0e08f730a851abba085e6cc7b4ec", | ||
| "taxonomy.idx:md5,f6c520613e1154909658f976498dd4a8", | ||
| "taxonomy.map:md5,5bb3f2192e925bca2e61e4b54f1671e0", | ||
| "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e" | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.10.2" | ||
| }, | ||
| "timestamp": "2025-01-09T16:49:09.883808608" | ||
| } | ||
| } |
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