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Update test snapshots
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+75
-75
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‎tests/default.nf.test.snap‎

Lines changed: 34 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -21,29 +21,29 @@
2121
"subject_a/amber",
2222
"subject_a/amber/placeholder",
2323
"subject_a/bamtools",
24-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools",
25-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.coverage.tsv",
26-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.flag_counts.tsv",
27-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.frag_length.tsv",
28-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.partition_stats.tsv",
29-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.summary.tsv",
30-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools",
31-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.coverage.tsv",
32-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.flag_counts.tsv",
33-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.frag_length.tsv",
34-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.partition_stats.tsv",
35-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.summary.tsv",
24+
"subject_a/bamtools/subject_a.normal",
25+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.coverage.tsv",
26+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.flag_counts.tsv",
27+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.frag_length.tsv",
28+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.partition_stats.tsv",
29+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.summary.tsv",
30+
"subject_a/bamtools/subject_a.tumor",
31+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.coverage.tsv",
32+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.flag_counts.tsv",
33+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.frag_length.tsv",
34+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.partition_stats.tsv",
35+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.summary.tsv",
3636
"subject_a/chord",
3737
"subject_a/chord/subject_a.tumor.chord.mutation_contexts.tsv",
3838
"subject_a/chord/subject_a.tumor.chord.prediction.tsv",
3939
"subject_a/cider",
40+
"subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz",
4041
"subject_a/cider/subject_a.tumor.cider.bam",
41-
"subject_a/cider/subject_a.tumor.cider.blastn_match.tsv.gz",
4242
"subject_a/cider/subject_a.tumor.cider.layout.gz",
4343
"subject_a/cider/subject_a.tumor.cider.locus_stats.tsv",
4444
"subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz",
45+
"subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz",
4546
"subject_a/cider/subject_a.tumor_rna.cider.bam",
46-
"subject_a/cider/subject_a.tumor_rna.cider.blastn_match.tsv.gz",
4747
"subject_a/cider/subject_a.tumor_rna.cider.layout.gz",
4848
"subject_a/cider/subject_a.tumor_rna.cider.locus_stats.tsv",
4949
"subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz",
@@ -277,6 +277,23 @@
277277
"subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz",
278278
"subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz",
279279
"subject_a/purple/subject_a.tumor.purple.sv.vcf.gz",
280+
"subject_a/sage",
281+
"subject_a/sage/germline",
282+
"subject_a/sage/germline/subject_a.normal.gene.coverage.tsv",
283+
"subject_a/sage/germline/subject_a.normal.sage.bqr.png",
284+
"subject_a/sage/germline/subject_a.normal.sage.bqr.tsv",
285+
"subject_a/sage/germline/subject_a.tumor.sage.bqr.png",
286+
"subject_a/sage/germline/subject_a.tumor.sage.bqr.tsv",
287+
"subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz",
288+
"subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz.tbi",
289+
"subject_a/sage/somatic",
290+
"subject_a/sage/somatic/subject_a.normal.sage.bqr.png",
291+
"subject_a/sage/somatic/subject_a.normal.sage.bqr.tsv",
292+
"subject_a/sage/somatic/subject_a.tumor.gene.coverage.tsv",
293+
"subject_a/sage/somatic/subject_a.tumor.sage.bqr.png",
294+
"subject_a/sage/somatic/subject_a.tumor.sage.bqr.tsv",
295+
"subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz",
296+
"subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi",
280297
"subject_a/sage_append",
281298
"subject_a/sage_append/germline",
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"subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz",
@@ -288,23 +305,6 @@
288305
"subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz",
289306
"subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz.tbi",
290307
"subject_a/sage_append/somatic/subject_a.tumor_query.sage.bqr.tsv",
291-
"subject_a/sage_calling",
292-
"subject_a/sage_calling/germline",
293-
"subject_a/sage_calling/germline/subject_a.normal.gene.coverage.tsv",
294-
"subject_a/sage_calling/germline/subject_a.normal.sage.bqr.png",
295-
"subject_a/sage_calling/germline/subject_a.normal.sage.bqr.tsv",
296-
"subject_a/sage_calling/germline/subject_a.tumor.sage.bqr.png",
297-
"subject_a/sage_calling/germline/subject_a.tumor.sage.bqr.tsv",
298-
"subject_a/sage_calling/germline/subject_a.tumor.sage.germline.vcf.gz",
299-
"subject_a/sage_calling/germline/subject_a.tumor.sage.germline.vcf.gz.tbi",
300-
"subject_a/sage_calling/somatic",
301-
"subject_a/sage_calling/somatic/subject_a.normal.sage.bqr.png",
302-
"subject_a/sage_calling/somatic/subject_a.normal.sage.bqr.tsv",
303-
"subject_a/sage_calling/somatic/subject_a.tumor.gene.coverage.tsv",
304-
"subject_a/sage_calling/somatic/subject_a.tumor.sage.bqr.png",
305-
"subject_a/sage_calling/somatic/subject_a.tumor.sage.bqr.tsv",
306-
"subject_a/sage_calling/somatic/subject_a.tumor.sage.somatic.vcf.gz",
307-
"subject_a/sage_calling/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi",
308308
"subject_a/sigs",
309309
"subject_a/sigs/placeholder",
310310
"subject_a/teal",
@@ -323,9 +323,9 @@
323323
]
324324
],
325325
"meta": {
326-
"nf-test": "0.9.2",
327-
"nextflow": "25.04.6"
326+
"nf-test": "0.9.3",
327+
"nextflow": "25.10.2"
328328
},
329-
"timestamp": "2025-08-12T16:05:52.737409"
329+
"timestamp": "2025-12-03T04:25:08.751931146"
330330
}
331331
}

‎tests/profile_test.nf.test.snap‎

Lines changed: 41 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -34,33 +34,33 @@
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"subject_a/amber/subject_a.tumor.amber.contamination.vcf.gz.tbi",
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"subject_a/amber/subject_a.tumor.amber.qc",
3636
"subject_a/bamtools",
37-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools",
38-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.coverage.tsv",
39-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.exon_medians.tsv",
40-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.flag_counts.tsv",
41-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.frag_length.tsv",
42-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.gene_coverage.tsv",
43-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.partition_stats.tsv",
44-
"subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.summary.tsv",
45-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools",
46-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.coverage.tsv",
47-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.exon_medians.tsv",
48-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.flag_counts.tsv",
49-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.frag_length.tsv",
50-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.gene_coverage.tsv",
51-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.partition_stats.tsv",
52-
"subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.summary.tsv",
37+
"subject_a/bamtools/subject_a.normal",
38+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.coverage.tsv",
39+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.exon_medians.tsv",
40+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.flag_counts.tsv",
41+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.frag_length.tsv",
42+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.gene_coverage.tsv",
43+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.partition_stats.tsv",
44+
"subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.summary.tsv",
45+
"subject_a/bamtools/subject_a.tumor",
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"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.coverage.tsv",
47+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.exon_medians.tsv",
48+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.flag_counts.tsv",
49+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.frag_length.tsv",
50+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.gene_coverage.tsv",
51+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.partition_stats.tsv",
52+
"subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.summary.tsv",
5353
"subject_a/chord",
5454
"subject_a/chord/subject_a.tumor.chord.mutation_contexts.tsv",
5555
"subject_a/chord/subject_a.tumor.chord.prediction.tsv",
5656
"subject_a/cider",
57+
"subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz",
5758
"subject_a/cider/subject_a.tumor.cider.bam",
58-
"subject_a/cider/subject_a.tumor.cider.blastn_match.tsv.gz",
5959
"subject_a/cider/subject_a.tumor.cider.layout.gz",
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"subject_a/cider/subject_a.tumor.cider.locus_stats.tsv",
6161
"subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz",
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"subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz",
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"subject_a/cider/subject_a.tumor_rna.cider.bam",
63-
"subject_a/cider/subject_a.tumor_rna.cider.blastn_match.tsv.gz",
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"subject_a/cider/subject_a.tumor_rna.cider.layout.gz",
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"subject_a/cider/subject_a.tumor_rna.cider.locus_stats.tsv",
6666
"subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz",
@@ -142,10 +142,10 @@
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"subject_a/linx/somatic_plots/all/subject_a.tumor.chr11.007.png",
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"subject_a/linx/somatic_plots/all/subject_a.tumor.chr19.000.png",
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"subject_a/linx/somatic_plots/all/subject_a.tumor.chr9.007.png",
145-
"subject_a/linx/somatic_plots/all/subject_a.tumor.cluster-0.sv2.003.png",
146-
"subject_a/linx/somatic_plots/all/subject_a.tumor.cluster-1.sv2.007.png",
145+
"subject_a/linx/somatic_plots/all/subject_a.tumor.cluster-0.resolved_type-SGL_PAIR_INS.sv_count-2.003.png",
146+
"subject_a/linx/somatic_plots/all/subject_a.tumor.cluster-1.resolved_type-RECIP_TRANS.sv_count-2.007.png",
147147
"subject_a/linx/somatic_plots/reportable",
148-
"subject_a/linx/somatic_plots/reportable/subject_a.tumor.cluster-1.sv2.007.png",
148+
"subject_a/linx/somatic_plots/reportable/subject_a.tumor.cluster-1.resolved_type-RECIP_TRANS.sv_count-2.007.png",
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"subject_a/linx/subject_a.tumor_linx.html",
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"subject_a/logs",
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"subject_a/logs/subject_a.amber.command.err",
@@ -365,8 +365,8 @@
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"subject_a/purple/plot/subject_a.tumor.somatic.clonality.png",
366366
"subject_a/purple/plot/subject_a.tumor.somatic.png",
367367
"subject_a/purple/plot/subject_a.tumor.somatic.rainfall.png",
368-
"subject_a/purple/plot/subject_a.tumor.somatic_data.tsv",
369368
"subject_a/purple/purple.version",
369+
"subject_a/purple/subject_a.tumor.purple.chromosome_arm.tsv",
370370
"subject_a/purple/subject_a.tumor.purple.cnv.gene.tsv",
371371
"subject_a/purple/subject_a.tumor.purple.cnv.somatic.tsv",
372372
"subject_a/purple/subject_a.tumor.purple.driver.catalog.germline.tsv",
@@ -386,6 +386,22 @@
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"subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz.tbi",
387387
"subject_a/purple/subject_a.tumor.purple.sv.vcf.gz",
388388
"subject_a/purple/subject_a.tumor.purple.sv.vcf.gz.tbi",
389+
"subject_a/sage",
390+
"subject_a/sage/germline",
391+
"subject_a/sage/germline/subject_a.normal.sage.bqr.png",
392+
"subject_a/sage/germline/subject_a.normal.sage.bqr.tsv",
393+
"subject_a/sage/germline/subject_a.tumor.sage.bqr.png",
394+
"subject_a/sage/germline/subject_a.tumor.sage.bqr.tsv",
395+
"subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz",
396+
"subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz.tbi",
397+
"subject_a/sage/somatic",
398+
"subject_a/sage/somatic/subject_a.normal.sage.bqr.png",
399+
"subject_a/sage/somatic/subject_a.normal.sage.bqr.tsv",
400+
"subject_a/sage/somatic/subject_a.tumor.sage.bqr.png",
401+
"subject_a/sage/somatic/subject_a.tumor.sage.bqr.tsv",
402+
"subject_a/sage/somatic/subject_a.tumor.sage.somatic.fit_variant.tsv",
403+
"subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz",
404+
"subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi",
389405
"subject_a/sage_append",
390406
"subject_a/sage_append/germline",
391407
"subject_a/sage_append/germline/subject_a.normal.sage.append.frag_lengths.tsv.gz",
@@ -397,22 +413,6 @@
397413
"subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz",
398414
"subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz.tbi",
399415
"subject_a/sage_append/somatic/subject_a.tumor_rna.sage.bqr.tsv",
400-
"subject_a/sage_calling",
401-
"subject_a/sage_calling/germline",
402-
"subject_a/sage_calling/germline/subject_a.normal.sage.bqr.png",
403-
"subject_a/sage_calling/germline/subject_a.normal.sage.bqr.tsv",
404-
"subject_a/sage_calling/germline/subject_a.tumor.sage.bqr.png",
405-
"subject_a/sage_calling/germline/subject_a.tumor.sage.bqr.tsv",
406-
"subject_a/sage_calling/germline/subject_a.tumor.sage.germline.vcf.gz",
407-
"subject_a/sage_calling/germline/subject_a.tumor.sage.germline.vcf.gz.tbi",
408-
"subject_a/sage_calling/somatic",
409-
"subject_a/sage_calling/somatic/subject_a.normal.sage.bqr.png",
410-
"subject_a/sage_calling/somatic/subject_a.normal.sage.bqr.tsv",
411-
"subject_a/sage_calling/somatic/subject_a.tumor.sage.bqr.png",
412-
"subject_a/sage_calling/somatic/subject_a.tumor.sage.bqr.tsv",
413-
"subject_a/sage_calling/somatic/subject_a.tumor.sage.somatic.fit_variant.tsv",
414-
"subject_a/sage_calling/somatic/subject_a.tumor.sage.somatic.vcf.gz",
415-
"subject_a/sage_calling/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi",
416416
"subject_a/sigs",
417417
"subject_a/sigs/subject_a.tumor.sig.allocation.tsv",
418418
"subject_a/sigs/subject_a.tumor.sig.snv_counts.csv",
@@ -432,9 +432,9 @@
432432
]
433433
],
434434
"meta": {
435-
"nf-test": "0.9.2",
436-
"nextflow": "25.04.6"
435+
"nf-test": "0.9.3",
436+
"nextflow": "25.10.2"
437437
},
438-
"timestamp": "2025-09-01T00:24:15.919488538"
438+
"timestamp": "2025-12-03T05:13:51.245667357"
439439
}
440440
}

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