Skip to content

Commit e4cfa09

Browse files
maxulyssemaxulysse
committed
update tests and snapshots
1 parent 056ce81 commit e4cfa09

9 files changed

+293
-293
lines changed

‎tests/default.nf.test.snap‎

Lines changed: 30 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -227,42 +227,42 @@
227227
},
228228
"star_salmon/samtools_stats": {
229229
"content": [
230-
"RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9",
231-
"RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8",
232-
"RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8",
233-
"RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8",
234-
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59",
235-
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1",
236-
"RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9",
237-
"RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1",
238-
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281",
239-
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d",
240-
"RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2",
241-
"RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d",
242-
"WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8",
243-
"WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f",
244-
"WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade",
245-
"WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f",
246-
"WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc",
247-
"WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68",
248-
"WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447",
249-
"WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68",
230+
"RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat",
231+
"RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats",
250232
"RAP1_IAA_30M_REP1.markdup.sorted.bam.stats",
233+
"RAP1_IAA_30M_REP1.sorted.bam.flagstat",
234+
"RAP1_IAA_30M_REP1.sorted.bam.idxstats",
251235
"RAP1_IAA_30M_REP1.sorted.bam.stats",
236+
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat",
237+
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats",
252238
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats",
239+
"RAP1_UNINDUCED_REP1.sorted.bam.flagstat",
240+
"RAP1_UNINDUCED_REP1.sorted.bam.idxstats",
253241
"RAP1_UNINDUCED_REP1.sorted.bam.stats",
242+
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat",
243+
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats",
254244
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats",
245+
"RAP1_UNINDUCED_REP2.sorted.bam.flagstat",
246+
"RAP1_UNINDUCED_REP2.sorted.bam.idxstats",
255247
"RAP1_UNINDUCED_REP2.sorted.bam.stats",
248+
"WT_REP1.markdup.sorted.bam.flagstat",
249+
"WT_REP1.markdup.sorted.bam.idxstats",
256250
"WT_REP1.markdup.sorted.bam.stats",
251+
"WT_REP1.sorted.bam.flagstat",
252+
"WT_REP1.sorted.bam.idxstats",
257253
"WT_REP1.sorted.bam.stats",
254+
"WT_REP2.markdup.sorted.bam.flagstat",
255+
"WT_REP2.markdup.sorted.bam.idxstats",
258256
"WT_REP2.markdup.sorted.bam.stats",
257+
"WT_REP2.sorted.bam.flagstat",
258+
"WT_REP2.sorted.bam.idxstats",
259259
"WT_REP2.sorted.bam.stats"
260260
],
261261
"meta": {
262262
"nf-test": "0.9.0",
263263
"nextflow": "24.04.4"
264264
},
265-
"timestamp": "2024-08-26T12:44:57.974787"
265+
"timestamp": "2024-08-26T18:42:17.143005"
266266
},
267267
"Params: default - stub": {
268268
"content": [
@@ -320,8 +320,6 @@
320320
"fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
321321
"featurecounts_biotype_plot-cnt.png:md5,4c66fce934b018143e7b8f6a1383d3f6",
322322
"featurecounts_biotype_plot-pct.png:md5,9191dc2dd130f22ad404d27e045d2304",
323-
"picard_deduplication-cnt.png:md5,52297225fca30daa61d3271754bdbc1a",
324-
"picard_deduplication-pct.png:md5,b2aa123cc65c933ca630d89c6f098550",
325323
"qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432",
326324
"qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e",
327325
"rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f",
@@ -332,8 +330,6 @@
332330
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d",
333331
"samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d",
334332
"samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f",
335-
"samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c",
336-
"samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2",
337333
"multiqc_report.html",
338334
"cutadapt_filtered_reads_plot-cnt.pdf",
339335
"cutadapt_filtered_reads_plot-pct.pdf",
@@ -417,6 +413,8 @@
417413
"fastqc_top_overrepresented_sequences_table-1.png",
418414
"fastqc_top_overrepresented_sequences_table.png",
419415
"general_stats_table.png",
416+
"picard_deduplication-cnt.png",
417+
"picard_deduplication-pct.png",
420418
"qualimap_genomic_origin-cnt.png",
421419
"qualimap_genomic_origin-pct.png",
422420
"rseqc_bam_stat.png",
@@ -437,6 +435,8 @@
437435
"samtools-flagstat-dp_Percentage_of_total.png",
438436
"samtools-flagstat-dp_Read_counts.png",
439437
"samtools-stats-dp.png",
438+
"samtools_alignment_plot-cnt.png",
439+
"samtools_alignment_plot-pct.png",
440440
"star_alignment_plot-cnt.png",
441441
"star_alignment_plot-pct.png",
442442
"star_salmon_deseq2_clustering-plot.png",
@@ -519,7 +519,7 @@
519519
"nf-test": "0.9.0",
520520
"nextflow": "24.04.4"
521521
},
522-
"timestamp": "2024-08-26T16:21:24.616733"
522+
"timestamp": "2024-08-26T18:42:16.932219"
523523
},
524524
"fastqc/raw": {
525525
"content": [
@@ -694,9 +694,7 @@
694694
"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
695695
"multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
696696
"multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71",
697-
"multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076",
698697
"multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
699-
"picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4",
700698
"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
701699
"picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
702700
"picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -707,7 +705,6 @@
707705
"samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
708706
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
709707
"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
710-
"samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20",
711708
"fastqc_top_overrepresented_sequences_table-1.txt",
712709
"fastqc_top_overrepresented_sequences_table.txt",
713710
"junction_saturation_known.txt",
@@ -716,6 +713,7 @@
716713
"multiqc_dupradar-section-plot.txt",
717714
"multiqc_fail_strand_check_table.txt",
718715
"multiqc_general_stats.txt",
716+
"multiqc_picard_dups.txt",
719717
"multiqc_rseqc_bam_stat.txt",
720718
"multiqc_rseqc_infer_experiment.txt",
721719
"multiqc_rseqc_junction_annotation.txt",
@@ -738,6 +736,7 @@
738736
"multiqc_star_salmon_deseq2_clustering-plot_3.txt",
739737
"multiqc_star_salmon_deseq2_clustering-plot_4.txt",
740738
"multiqc_star_salmon_deseq2_pca-plot.txt",
739+
"picard_deduplication.txt",
741740
"qualimap_genomic_origin.txt",
742741
"qualimap_rnaseq_genome_results.txt",
743742
"rseqc_bam_stat.txt",
@@ -757,14 +756,15 @@
757756
"samtools-flagstat-dp_Percentage_of_total.txt",
758757
"samtools-flagstat-dp_Read_counts.txt",
759758
"samtools-stats-dp.txt",
759+
"samtools_alignment_plot.txt",
760760
"star_alignment_plot.txt",
761761
"star_summary_table.txt"
762762
],
763763
"meta": {
764764
"nf-test": "0.9.0",
765765
"nextflow": "24.04.4"
766766
},
767-
"timestamp": "2024-08-26T16:21:24.483792"
767+
"timestamp": "2024-08-26T18:42:16.785525"
768768
},
769769
"star_salmon/deseq2_qc": {
770770
"content": [

‎tests/featurecounts_group_type.nf.test.snap‎

Lines changed: 30 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -122,9 +122,7 @@
122122
"multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
123123
"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
124124
"multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
125-
"multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076",
126125
"multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
127-
"picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4",
128126
"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
129127
"picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
130128
"picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -135,7 +133,6 @@
135133
"samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
136134
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
137135
"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
138-
"samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20",
139136
"fastqc_top_overrepresented_sequences_table-1.txt",
140137
"fastqc_top_overrepresented_sequences_table.txt",
141138
"junction_saturation_known.txt",
@@ -144,6 +141,7 @@
144141
"multiqc_dupradar-section-plot.txt",
145142
"multiqc_fail_strand_check_table.txt",
146143
"multiqc_general_stats.txt",
144+
"multiqc_picard_dups.txt",
147145
"multiqc_rseqc_bam_stat.txt",
148146
"multiqc_rseqc_infer_experiment.txt",
149147
"multiqc_rseqc_junction_annotation.txt",
@@ -166,6 +164,7 @@
166164
"multiqc_star_salmon_deseq2_clustering-plot_3.txt",
167165
"multiqc_star_salmon_deseq2_clustering-plot_4.txt",
168166
"multiqc_star_salmon_deseq2_pca-plot.txt",
167+
"picard_deduplication.txt",
169168
"qualimap_genomic_origin.txt",
170169
"qualimap_rnaseq_genome_results.txt",
171170
"rseqc_bam_stat.txt",
@@ -185,14 +184,15 @@
185184
"samtools-flagstat-dp_Percentage_of_total.txt",
186185
"samtools-flagstat-dp_Read_counts.txt",
187186
"samtools-stats-dp.txt",
187+
"samtools_alignment_plot.txt",
188188
"star_alignment_plot.txt",
189189
"star_summary_table.txt"
190190
],
191191
"meta": {
192192
"nf-test": "0.9.0",
193193
"nextflow": "24.04.4"
194194
},
195-
"timestamp": "2024-08-26T16:29:22.875142"
195+
"timestamp": "2024-08-26T18:50:10.937365"
196196
},
197197
"trimgalore": {
198198
"content": [
@@ -367,42 +367,42 @@
367367
},
368368
"star_salmon/samtools_stats": {
369369
"content": [
370-
"RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9",
371-
"RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8",
372-
"RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8",
373-
"RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8",
374-
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59",
375-
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1",
376-
"RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9",
377-
"RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1",
378-
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281",
379-
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d",
380-
"RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2",
381-
"RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d",
382-
"WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8",
383-
"WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f",
384-
"WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade",
385-
"WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f",
386-
"WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc",
387-
"WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68",
388-
"WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447",
389-
"WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68",
370+
"RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat",
371+
"RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats",
390372
"RAP1_IAA_30M_REP1.markdup.sorted.bam.stats",
373+
"RAP1_IAA_30M_REP1.sorted.bam.flagstat",
374+
"RAP1_IAA_30M_REP1.sorted.bam.idxstats",
391375
"RAP1_IAA_30M_REP1.sorted.bam.stats",
376+
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat",
377+
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats",
392378
"RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats",
379+
"RAP1_UNINDUCED_REP1.sorted.bam.flagstat",
380+
"RAP1_UNINDUCED_REP1.sorted.bam.idxstats",
393381
"RAP1_UNINDUCED_REP1.sorted.bam.stats",
382+
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat",
383+
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats",
394384
"RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats",
385+
"RAP1_UNINDUCED_REP2.sorted.bam.flagstat",
386+
"RAP1_UNINDUCED_REP2.sorted.bam.idxstats",
395387
"RAP1_UNINDUCED_REP2.sorted.bam.stats",
388+
"WT_REP1.markdup.sorted.bam.flagstat",
389+
"WT_REP1.markdup.sorted.bam.idxstats",
396390
"WT_REP1.markdup.sorted.bam.stats",
391+
"WT_REP1.sorted.bam.flagstat",
392+
"WT_REP1.sorted.bam.idxstats",
397393
"WT_REP1.sorted.bam.stats",
394+
"WT_REP2.markdup.sorted.bam.flagstat",
395+
"WT_REP2.markdup.sorted.bam.idxstats",
398396
"WT_REP2.markdup.sorted.bam.stats",
397+
"WT_REP2.sorted.bam.flagstat",
398+
"WT_REP2.sorted.bam.idxstats",
399399
"WT_REP2.sorted.bam.stats"
400400
],
401401
"meta": {
402402
"nf-test": "0.9.0",
403403
"nextflow": "24.04.4"
404404
},
405-
"timestamp": "2024-08-26T14:18:39.635582"
405+
"timestamp": "2024-08-26T18:50:11.105038"
406406
},
407407
"salmon/deseq2_qc": {
408408
"content": [
@@ -469,8 +469,6 @@
469469
"fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054",
470470
"fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
471471
"fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
472-
"picard_deduplication-cnt.png:md5,52297225fca30daa61d3271754bdbc1a",
473-
"picard_deduplication-pct.png:md5,b2aa123cc65c933ca630d89c6f098550",
474472
"qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432",
475473
"qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e",
476474
"rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f",
@@ -481,8 +479,6 @@
481479
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d",
482480
"samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d",
483481
"samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f",
484-
"samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c",
485-
"samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2",
486482
"multiqc_report.html",
487483
"cutadapt_filtered_reads_plot-cnt.pdf",
488484
"cutadapt_filtered_reads_plot-pct.pdf",
@@ -564,6 +560,8 @@
564560
"fastqc_top_overrepresented_sequences_table-1.png",
565561
"fastqc_top_overrepresented_sequences_table.png",
566562
"general_stats_table.png",
563+
"picard_deduplication-cnt.png",
564+
"picard_deduplication-pct.png",
567565
"qualimap_genomic_origin-cnt.png",
568566
"qualimap_genomic_origin-pct.png",
569567
"rseqc_bam_stat.png",
@@ -584,6 +582,8 @@
584582
"samtools-flagstat-dp_Percentage_of_total.png",
585583
"samtools-flagstat-dp_Read_counts.png",
586584
"samtools-stats-dp.png",
585+
"samtools_alignment_plot-cnt.png",
586+
"samtools_alignment_plot-pct.png",
587587
"star_alignment_plot-cnt.png",
588588
"star_alignment_plot-pct.png",
589589
"star_salmon_deseq2_clustering-plot.png",
@@ -664,7 +664,7 @@
664664
"nf-test": "0.9.0",
665665
"nextflow": "24.04.4"
666666
},
667-
"timestamp": "2024-08-26T16:29:22.943986"
667+
"timestamp": "2024-08-26T18:50:11.011282"
668668
},
669669
"star_salmon/picard_metrics": {
670670
"content": [

0 commit comments

Comments
 (0)