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115 changes: 115 additions & 0 deletions
115
subworkflows/local/starfusion_workflow/tests/main.nf.test
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| nextflow_workflow { | ||
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| name "Test Subworkflow STARFUSION_WORKFLOW" | ||
| script "../main.nf" | ||
| workflow "STARFUSION_WORKFLOW" | ||
| tag "subworkflow" | ||
| tag "star" | ||
| tag "star/genomegenerate" | ||
| tag "star/align" | ||
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| test("STARFUSION_WORKFLOW - Homo sapiens - FASTQs minigenome") { | ||
| config './nextflow.config' | ||
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| setup { | ||
| run("STAR_GENOMEGENERATE") { | ||
| script "../../../../modules/nf-core/star/genomegenerate/main.nf" | ||
| process { | ||
| """ | ||
| // FASTA | ||
| input[0] = Channel.fromPath( | ||
| "https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.fa", checkIfExists: true | ||
| ) | ||
| .map{ [[id: it.getName() ], it ]} | ||
| // GTF | ||
| input[1] = Channel.fromPath( | ||
| "https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.gtf", checkIfExists: true | ||
| ) | ||
| .map{ [[id: it.getName() ], it ]} | ||
| """ | ||
| } | ||
| } | ||
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| run("STARFUSION_BUILD") { | ||
| script "../../../../modules/local/starfusion/build/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'minigenome fasta' ], | ||
| file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.fa") | ||
| ] | ||
| input[1] = [ | ||
| [ id:'minigenome gtf' ], | ||
| file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.gtf") | ||
| ] | ||
| input [2] = file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz") | ||
| input [3] = "human" | ||
| """ | ||
| } | ||
| } | ||
| } | ||
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| when { | ||
| workflow { | ||
| """ | ||
| // ch_reads | ||
| input[0] = Channel.of( | ||
| [ | ||
| [ id: "test_fastqs" ], | ||
| [ | ||
| file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_1.fastq.gz", checkIfExists: true), | ||
| file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_2.fastq.gz", checkIfExists: true) | ||
| ] | ||
| ] ) | ||
| // ch_gtf | ||
| input[1] = | ||
| Channel.fromPath( | ||
| "https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.gtf", checkIfExists: true | ||
| ) | ||
| .map{ [ [ id: it.name ], it ] } | ||
| // ch_starindex_ref | ||
| input[2] = STAR_GENOMEGENERATE.out.index | ||
| // ch_fasta | ||
| input[3] = | ||
| Channel.fromPath( | ||
| "https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.fa", checkIfExists: true | ||
| ) | ||
| .map{ [ [ id: it.name ], it ] } | ||
| // ch_starfusion_ref | ||
| input[4] = STARFUSION_BUILD.out.reference | ||
| """ | ||
| } | ||
| params { | ||
| starfusion = true | ||
| cram = 'starfusion' | ||
| outdir = "$outputDir" | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot( | ||
| workflow.out.fusions, | ||
| file(workflow.out.star_stats[0][1]).name, | ||
| workflow.out.star_gene_count, | ||
| workflow.out.ch_bam_sorted, | ||
| workflow.out.ch_bam_sorted_indexed, | ||
| workflow.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
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| } |
38 changes: 38 additions & 0 deletions
38
subworkflows/local/starfusion_workflow/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,38 @@ | ||
| { | ||
| "STARFUSION_WORKFLOW - Homo sapiens - FASTQs minigenome": { | ||
| "content": [ | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test_fastqs" | ||
| }, | ||
| "test_fastqs.starfusion.fusion_predictions.tsv:md5,abe17134a231642edf9351e4964e8a97" | ||
| ] | ||
| ], | ||
| "test_fastqs.Log.final.out", | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test_fastqs" | ||
| }, | ||
| "test_fastqs.ReadsPerGene.out.tab:md5,8e0d42deeea09924d5c7ba3147bbfd78" | ||
| ] | ||
| ], | ||
| [ | ||
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| ], | ||
| [ | ||
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| ], | ||
| [ | ||
| "versions.yml:md5,afde4f2fd6056df81e322b3c35ab7a8a", | ||
| "versions.yml:md5,e53f1ec32bc78a33f99892e42274833a" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.3" | ||
| }, | ||
| "timestamp": "2024-12-23T18:25:52.838411738" | ||
| } | ||
| } |
37 changes: 37 additions & 0 deletions
37
subworkflows/local/starfusion_workflow/tests/nextflow.config
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| @@ -0,0 +1,37 @@ | ||
| process { | ||
| withName: 'STAR_FOR_STARFUSION' { | ||
| ext.args = '--twopassMode Basic \ | ||
| --outReadsUnmapped None \ | ||
| --readFilesCommand zcat \ | ||
| --outSAMtype BAM SortedByCoordinate \ | ||
| --outSAMstrandField intronMotif \ | ||
| --outSAMunmapped Within \ | ||
| --chimSegmentMin 12 \ | ||
| --chimJunctionOverhangMin 8 \ | ||
| --chimOutJunctionFormat 1 \ | ||
| --alignSJDBoverhangMin 10 \ | ||
| --alignMatesGapMax 100000 \ | ||
| --alignIntronMax 100000 \ | ||
| --alignSJstitchMismatchNmax 5 -1 5 5 \ | ||
| --chimMultimapScoreRange 3 \ | ||
| --chimScoreJunctionNonGTAG -4 \ | ||
| --chimMultimapNmax 20 \ | ||
| --chimNonchimScoreDropMin 10 \ | ||
| --peOverlapNbasesMin 12 \ | ||
| --peOverlapMMp 0.1 \ | ||
| --alignInsertionFlush Right \ | ||
| --alignSplicedMateMapLminOverLmate 0 \ | ||
| --alignSplicedMateMapLmin 30 \ | ||
| --chimOutType Junctions \ | ||
| --quantMode GeneCounts' | ||
| } | ||
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| withName: 'SAMTOOLS_INDEX_FOR_STARFUSION_CRAM' { | ||
| ext.prefix = { "${meta.id}.star_for_starfusion.Aligned.sortedByCoord.out" } | ||
| } | ||
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| withName: 'SAMTOOLS_VIEW_FOR_STARFUSION' { | ||
| ext.args = { "--output-fmt cram" } | ||
| ext.prefix = { "${meta.id}.star_for_starfusion.Aligned.sortedByCoord.out" } | ||
| } | ||
| } |