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Merge pull request #583 from atrigila/fusioninspector
Add nf-test to `STARFUSION_BUILD` and refactor module
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| nextflow_process { | ||
|
|
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| name "Test Process STARFUSION_BUILD" | ||
| script "../main.nf" | ||
| process "STARFUSION_BUILD" | ||
|
|
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| test("STARFUSION_BUILD - human - minigenome") { | ||
|
|
||
| when { | ||
| 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" | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assert snapshot( | ||
| path(process.out.reference[0][1]).resolve("AnnotFilterRule.pm"), | ||
| path(process.out.reference[0][1]).resolve("blast_pairs.dat.gz").exists(), | ||
| path(process.out.reference[0][1]).resolve("blast_pairs.idx").exists(), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/annotfiltrule_cp.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/blast_pairs.idx.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/cp_gene_blast_pairs.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/cp_pfam_dat.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/cp_ref_annot_cdna.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/fusion_annot_lib.cp.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/_fusion_annot_lib.idx.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/index_pfam_hits.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/index_ref_annot_cdna.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/makeblastdb.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/mm2_genome_idx.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/mm2.splice_bed.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/_prot_info_db.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/ref_annot.gtf.gene_spans.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/ref_annot.gtf.mini.sortu.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/ref_annot.gtf.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/ref_genome_fai.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/ref_genome.fa.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/trans.blast.dat.cp.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/trans.blast.dat.index.ok"), | ||
| path(process.out.reference[0][1]).resolve("__chkpts/validate_ctat_genome_lib.ok"), | ||
| path(process.out.reference[0][1]).resolve("fusion_annot_lib.gz"), | ||
| path(process.out.reference[0][1]).resolve("fusion_annot_lib.idx").exists(), | ||
| path(process.out.reference[0][1]).resolve("pfam_domains.dbm").exists(), | ||
| path(process.out.reference[0][1]).resolve("PFAM.domtblout.dat.gz").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.cdna.fa").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.cdna.fa.idx").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.cds").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.cdsplus.fa").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.cdsplus.fa.idx").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.gtf"), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.gtf.gene_spans").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.gtf.mini.sortu"), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.gtf.mm2.splice.bed"), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.pep").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_annot.prot_info.dbm").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.fai"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.mm2"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.ndb"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.nhr"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.nin").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.njs").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.not"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.nsq"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.ntf"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.nto"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/build.ok"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/chrLength.txt"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/chrNameLength.txt"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/chrName.txt"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/chrStart.txt"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/exonGeTrInfo.tab"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/exonInfo.tab"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/geneInfo.tab"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/Genome"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/genomeParameters.txt").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/Log.out").exists(), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/SA"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/SAindex"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/sjdbInfo.txt"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/sjdbList.fromGTF.out.tab"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/sjdbList.out.tab"), | ||
| path(process.out.reference[0][1]).resolve("ref_genome.fa.star.idx/transcriptInfo.tab"), | ||
| path(process.out.reference[0][1]).resolve("trans.blast.align_coords.align_coords.dat"), | ||
| path(process.out.reference[0][1]).resolve("trans.blast.align_coords.align_coords.dbm").exists(), | ||
| path(process.out.reference[0][1]).resolve("trans.blast.dat.gz"), | ||
| process.out.versions | ||
| ).match() | ||
| } | ||
|
|
||
| } | ||
|
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| test("STARFUSION_BUILD - human - minigenome - stub") { | ||
|
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| options "-stub" | ||
|
|
||
| when { | ||
| 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" | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assert snapshot(process.out).match() | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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