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Merge pull request #601 from atrigila/fusioninspector_nftest
Add nf-test for local module `FUSIONINSPECTOR`
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,147 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process FUSIONINSPECTOR" | ||
| script "../main.nf" | ||
| process "FUSIONINSPECTOR" | ||
| tag "modules" | ||
| tag "modules_local" | ||
| tag "fusioninspector" | ||
|
|
||
| test("FUSIONINSPECTOR") { | ||
| config './nextflow.config' | ||
|
|
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| setup { | ||
| run("STARFUSION_BUILD") { | ||
| script "../../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" | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| [ | ||
| file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_1.fastq.gz"), | ||
| file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_2.fastq.gz") | ||
| ], // reads | ||
| [ | ||
| file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt") | ||
| ] | ||
| ] | ||
| input[1] = STARFUSION_BUILD.out.reference.map { it[1] } | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
|
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| def unstableFiles = [ | ||
| "test.bed", | ||
| "test.consolidated.bam", | ||
| "test.consolidated.bam.bai", | ||
| "test.junction_reads.bam", | ||
| "test.junction_reads.bam.bai", | ||
| "test.spanning_reads.bam", | ||
| "Log.final.out", | ||
| "Log.out", | ||
| "microH.dat", | ||
| "test.fusion_preds.coalesced.summary", | ||
| "test.fusion_preds.coalesced.summary.EMadj", | ||
| "test.fusion_preds.coalesced.summary.min_frag_thresh", | ||
| "test.fusion_preds.coalesced.summary.wSpliceInfo", | ||
| "test.fusion_preds.coalesced.summary.wSpliceInfo.post_blast_filter", | ||
| "test.fusion_preds.coalesced.summary.wSpliceInfo.post_blast_filter.post_promisc_filter", | ||
| "test.fusion_preds.coalesced.summary.fusion_junction_reads_acc", | ||
| "test.fusion_preds.coalesced.summary.fusion_spanning_reads_acc", | ||
| "test.post_blast_and_promiscuity_filter", | ||
| "test.post_blast_and_promiscuity_filter.EMadj", | ||
| "test.post_blast_and_promiscuity_filter.EMadj.FFPM", | ||
| "test.post_blast_and_promiscuity_filter.EMadj.FFPM.wMicroH", | ||
| "test.post_blast_and_promiscuity_filter.EMadj.FFPM.wMicroH.annotated", | ||
| "test.post_blast_and_promiscuity_filter.EMadj.FFPM.wMicroH.annotated.coding_effect", | ||
| "test.star.cSorted.dupsMarked.bam", | ||
| "test.star.cSorted.dupsMarked.bam.bai", | ||
| "test.star.cSorted.dupsMarked.bam.fusion_junction_info", | ||
| "test.star.cSorted.dupsMarked.bam.fusion_spanning_info", | ||
| "test.star.cSorted.dupsMarked.bam.read_align_counts", | ||
| "test.star.cSorted.dupsMarked.bam.read_align_counts.idx", | ||
| "test.star.cSorted.dupsMarked.bam.spanning_reads_want.idx", | ||
| "test.star.sortedByCoord.out.bam", | ||
| "test.star.sortedByCoord.out.bam.bai", | ||
| "test.fusion_preds.coalesced.summary.EMadj.min_frag_thresh", | ||
| "test.fusion_preds.coalesced.summary.fusion_junction_read_accs", | ||
| "test.fusion_preds.coalesced.summary.fusion_spanning_read_accs", | ||
| "test.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo", | ||
| "test.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter", | ||
| "test.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter" | ||
| ] | ||
|
|
||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| file(process.out.tsv[0][1]).name, | ||
| process.out.tsv_coding_effect, // TODO: These files do not seem to be produced. Consult Annick. | ||
| process.out.out_gtf, // TODO: These files do not seem to be produced. Consult Annick. | ||
| file(process.out.log[0][1]).name, | ||
| file(process.out.html[0][1]).name, | ||
| file(process.out.abridged_tsv[0][1]).name, | ||
| file(process.out.igv_inputs[0][1]).listFiles().findAll { file -> !unstableFiles.contains(file.name) }, | ||
| file(process.out.fi_workdir[0][1]).listFiles().findAll { file -> !unstableFiles.contains(file.name) }, | ||
| file(process.out.igv_inputs[0][1]).list().findAll { file -> !unstableFiles.contains(file) }, | ||
| file(process.out.fi_workdir[0][1]).list().findAll { file -> !unstableFiles.contains(file) }, | ||
| process.out.chckpts_dir, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
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| test("FUSIONINSPECTOR stub") { | ||
| options "-stub" | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| [ | ||
| file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_1.fastq.gz"), | ||
| file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_2.fastq.gz") | ||
| ], // reads | ||
| [ | ||
| file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt") | ||
| ] | ||
| ] | ||
| input[1] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out | ||
| ).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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