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Merge pull request nf-core#1239 from maxulysse/align_star
ALIGN_STAR - add nf-test tests
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| @@ -0,0 +1,159 @@ | ||
| nextflow_workflow { | ||
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| name "Test Subworkflow ALIGN_STAR" | ||
| script "../main.nf" | ||
| workflow "ALIGN_STAR" | ||
| config "./nextflow.config" | ||
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| tag "ALIGN_STAR" | ||
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| tag "star/align" | ||
| tag "star/genomegenerate" | ||
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| tag "STAR_ALIGN_IGENOMES" | ||
| tag "STAR_GENOMEGENERATE_IGENOMES" | ||
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| tag "BAM_SORT_STATS_SAMTOOLS" | ||
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| test("star - no igenomes") { | ||
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| setup { | ||
| run("STAR_GENOMEGENERATE") { | ||
| script "../../../../modules/nf-core/star/genomegenerate/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test_fasta' ], | ||
| [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] | ||
| ]) | ||
| input[1] = Channel.of([ | ||
| [ id:'test_gtf' ], | ||
| [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
| } | ||
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| when { | ||
| workflow { | ||
| """ | ||
| star_ignore_sjdbgtf = false | ||
| seq_platform = 'illumina' | ||
| seq_center = false | ||
| is_aws_igenome = false | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false ], // meta map | ||
| [ | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) | ||
| ] | ||
| ]) | ||
| input[1] = STAR_GENOMEGENERATE.out.index | ||
| input[2] = Channel.of([ | ||
| [ id:'test_gtf' ], | ||
| [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] | ||
| ]) | ||
| input[3] = star_ignore_sjdbgtf | ||
| input[4] = seq_platform | ||
| input[5] = seq_center | ||
| input[6] = is_aws_igenome | ||
| input[7] = Channel.of([ | ||
| [ id:'test_fasta' ], | ||
| [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success}, | ||
| { assert snapshot(file(workflow.out.log_final[0][1]).name).match("without igenomes - log_final") }, | ||
| { assert snapshot(file(workflow.out.log_out[0][1]).name).match("without igenomes - log_out") }, | ||
| { assert snapshot(workflow.out.bai).match("without igenomes - bai")}, | ||
| { assert snapshot(workflow.out.bam).match("without igenomes - bam")}, | ||
| { assert snapshot(workflow.out.bam_sorted).match("without igenomes - bam_sorted")}, | ||
| { assert snapshot(workflow.out.bam_transcript).match("without igenomes - bam_transcript")}, | ||
| { assert snapshot(workflow.out.csi).match("without igenomes - csi")}, | ||
| { assert snapshot(workflow.out.log_progress).match("without igenomes - log_progress")}, | ||
| { assert snapshot(workflow.out.fastq).match("without igenomes - fastq")}, | ||
| { assert snapshot(workflow.out.flagstat).match("without igenomes - flagstat")}, | ||
| { assert snapshot(workflow.out.idxstats).match("without igenomes - idxstats")}, | ||
| { assert snapshot(workflow.out.orig_bam).match("without igenomes - orig_bam")}, | ||
| { assert snapshot(workflow.out.stats).match("without igenomes - stats")}, | ||
| { assert snapshot(workflow.out.tab).match("without igenomes - tab")}, | ||
| { assert snapshot(workflow.out.versions).match("without igenomes - versions")} | ||
| ) | ||
| } | ||
| } | ||
| test("star - with igenomes") { | ||
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| setup { | ||
| run("STAR_GENOMEGENERATE_IGENOMES") { | ||
| script "../../../../modules/local/star_genomegenerate_igenomes/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) | ||
| input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)]) | ||
| """ | ||
| } | ||
| } | ||
| } | ||
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| when { | ||
| workflow { | ||
| """ | ||
| star_ignore_sjdbgtf = false | ||
| seq_platform = 'illumina' | ||
| seq_center = false | ||
| is_aws_igenome = true | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false ], // meta map | ||
| [ | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) | ||
| ] | ||
| ]) | ||
| input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] } | ||
| input[2] = Channel.of([ | ||
| [ id:'test_gtf' ], | ||
| [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] | ||
| ]) | ||
| input[3] = star_ignore_sjdbgtf | ||
| input[4] = seq_platform | ||
| input[5] = seq_center | ||
| input[6] = is_aws_igenome | ||
| input[7] = Channel.of([ | ||
| [ id:'test_fasta' ], | ||
| [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success}, | ||
| { assert snapshot(file(workflow.out.log_final[0][1]).name).match("with igenomes - log_final") }, | ||
| { assert snapshot(file(workflow.out.log_out[0][1]).name).match("with igenomes - log_out") }, | ||
| { assert snapshot(workflow.out.bai).match("with igenomes - bai")}, | ||
| { assert snapshot(workflow.out.bam).match("with igenomes - bam")}, | ||
| { assert snapshot(workflow.out.bam_sorted).match("with igenomes - bam_sorted")}, | ||
| { assert snapshot(workflow.out.bam_transcript).match("with igenomes - bam_transcript")}, | ||
| { assert snapshot(workflow.out.csi).match("with igenomes - csi")}, | ||
| { assert snapshot(workflow.out.log_progress).match("with igenomes - log_progress")}, | ||
| { assert snapshot(workflow.out.fastq).match("with igenomes - fastq")}, | ||
| { assert snapshot(workflow.out.flagstat).match("with igenomes - flagstat")}, | ||
| { assert snapshot(workflow.out.idxstats).match("with igenomes - idxstats")}, | ||
| { assert snapshot(workflow.out.orig_bam).match("with igenomes - orig_bam")}, | ||
| { assert snapshot(workflow.out.stats).match("with igenomes - stats")}, | ||
| { assert snapshot(workflow.out.tab).match("with igenomes - tab")}, | ||
| { assert snapshot(workflow.out.versions).match("with igenomes - versions")} | ||
| ) | ||
| } | ||
| } | ||
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| } |
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