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Modify DAS_Tool input structure, bump version, switch to nf-test (#7163)
* Update DAS_Tool and add nf-test tests * Remove old tests * Fix tags and remove dastool from pytest modules YAML * Fix meta.yml * Update snapshot * Update test * Add stubs to dastool/dastool, dastool/fastatocontig2bin, and metabat2/metabat2. Add tests for dastool stub runs. Add test for log file output from dastool/dastool * Fix linting + change test ext args config to match documentation * Move config inside tests as it's not needed for the stub * Deprecate dastool/fastatoscaffolds2bin * Fix test
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| Original file line number | Diff line number | Diff line change |
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@@ -2,4 +2,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::das_tool=1.1.6 | ||
| - bioconda::das_tool=1.1.7 | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,177 @@ | ||
| nextflow_process { | ||
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| name "Test Process DASTOOL_DASTOOL" | ||
| script "../main.nf" | ||
| process "DASTOOL_DASTOOL" | ||
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "dastool" | ||
| tag "dastool/dastool" | ||
| tag "dastool/fastatocontig2bin" | ||
| tag "metabat2/metabat2" | ||
| tag "metabat2/jgisummarizebamcontigdepths" | ||
| tag "prodigal" | ||
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| setup { | ||
| run("METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS") { | ||
| script "../../../metabat2/jgisummarizebamcontigdepths/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + "genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam", checkIfExists: true), | ||
| file(params.modules_testdata_base_path + "genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai", checkIfExists: true), | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| run("METABAT2_METABAT2") { | ||
| script "../../../metabat2/metabat2/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false ], | ||
| file(params.modules_testdata_base_path + "genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz", checkIfExists: true) | ||
| ]).join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth) | ||
| """ | ||
| } | ||
| } | ||
| run("DASTOOL_FASTATOCONTIG2BIN") { | ||
| script "../../fastatocontig2bin/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = METABAT2_METABAT2.out.fasta.collect() | ||
| input[1] = "fa" | ||
| """ | ||
| } | ||
| } | ||
| run("PRODIGAL") { | ||
| script "../../../prodigal/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false ], | ||
| file(params.modules_testdata_base_path + "genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz", checkIfExists: true) | ||
| ]) | ||
| input[1] = "gff" | ||
| """ | ||
| } | ||
| } | ||
| } | ||
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| test("dastool dastool - bacteroides fragilis - noproteins") { | ||
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| config "./nextflow.config" | ||
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| when { | ||
| params { | ||
| module_args = '--write_bins --write_bin_evals' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false ], | ||
| file(params.modules_testdata_base_path + "genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz", checkIfExists: true) | ||
| ]).join(DASTOOL_FASTATOCONTIG2BIN.out.fastatocontig2bin) | ||
| .map { meta, contigs, c2b -> [ meta, contigs, c2b, [] ]} | ||
| input[1] = [] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert path(process.out.log.get(0).get(1)).text.contains("Dereplicating, aggregating, and scoring bins") }, | ||
| { assert path(process.out.fasta_proteins.get(0).get(1)).text.contains("MKIGIITICKVNNYGAELQAFATQKKLEQMGHNAEIINYLYYKDWHFKDTPLSQPFVPLD") }, | ||
| { assert snapshot( | ||
| process.out.summary, | ||
| process.out.contig2bin, | ||
| process.out.eval, | ||
| process.out.bins, | ||
| process.out.pdfs, | ||
| process.out.candidates_faa, | ||
| process.out.fasta_archaea_scg, | ||
| process.out.fasta_bacteria_scg, | ||
| process.out.b6, | ||
| process.out.seqlength, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
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| } | ||
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| test("dastool dastool - bacteroides fragilis - proteins") { | ||
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| config "./nextflow.config" | ||
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| when { | ||
| params { | ||
| module_args = '--write_bins --write_bin_evals' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false ], | ||
| file(params.modules_testdata_base_path + "genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz", checkIfExists: true) | ||
| ]) | ||
| .join(DASTOOL_FASTATOCONTIG2BIN.out.fastatocontig2bin) | ||
| .join(PRODIGAL.out.amino_acid_fasta) | ||
| input[1] = [] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert path(process.out.log.get(0).get(1)).text.contains("Dereplicating, aggregating, and scoring bins") }, | ||
| { assert snapshot( | ||
| process.out.summary, | ||
| process.out.contig2bin, | ||
| process.out.eval, | ||
| process.out.bins, | ||
| process.out.pdfs, | ||
| process.out.fasta_proteins, | ||
| process.out.candidates_faa, | ||
| process.out.fasta_archaea_scg, | ||
| process.out.fasta_bacteria_scg, | ||
| process.out.b6, | ||
| process.out.seqlength, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
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| } | ||
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| test("dastool dastool - bacteroides fragilis - stub") { | ||
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| options "-stub" | ||
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| when { | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false ], | ||
| file(params.modules_testdata_base_path + "genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz", checkIfExists: true) | ||
| ]) | ||
| .join(DASTOOL_FASTATOCONTIG2BIN.out.fastatocontig2bin) | ||
| .join(PRODIGAL.out.amino_acid_fasta) | ||
| input[1] = [] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
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| } | ||
| } | ||
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