Skip to content

Commit 8679eda

Browse files
maxulyssemaxulysse
authored
Merge pull request #1360 from maxulysse/moar_snapshots
Snapshot all files (content or file name when not stable)
2 parents 715adf1 + e4cfa09 commit 8679eda

21 files changed

+15411
-51
lines changed

‎CHANGELOG.md‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -115,6 +115,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
115115
- [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc
116116
- [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests
117117
- [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround
118+
- [PR #1360](https://github.com/nf-core/rnaseq/pull/1360) - More complete snapshots for pipeline level tests
118119
- [PR #1361](https://github.com/nf-core/rnaseq/pull/1361) - Animate subway map
119120
- [PR #1362](https://github.com/nf-core/rnaseq/pull/1362) - Move multiqc module prefix for nf-test to module
120121

‎tests/default.nf.test‎

Lines changed: 922 additions & 15 deletions
Large diffs are not rendered by default.

‎tests/default.nf.test.snap‎

Lines changed: 1071 additions & 26 deletions
Large diffs are not rendered by default.

‎tests/featurecounts_group_type.nf.test‎

Lines changed: 915 additions & 1 deletion
Large diffs are not rendered by default.

‎tests/featurecounts_group_type.nf.test.snap‎

Lines changed: 1044 additions & 0 deletions
Large diffs are not rendered by default.

‎tests/hisat2.nf.test‎

Lines changed: 843 additions & 2 deletions
Large diffs are not rendered by default.

‎tests/hisat2.nf.test.snap‎

Lines changed: 961 additions & 0 deletions
Large diffs are not rendered by default.

‎tests/kallisto.nf.test‎

Lines changed: 205 additions & 1 deletion
Large diffs are not rendered by default.

‎tests/kallisto.nf.test.snap‎

Lines changed: 241 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,241 @@
1+
{
2+
"multiqc_data": {
3+
"content": [
4+
"cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
5+
"cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
6+
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
7+
"fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
8+
"fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
9+
"fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
10+
"fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
11+
"fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
12+
"fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
13+
"fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
14+
"fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c",
15+
"fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
16+
"fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
17+
"multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee",
18+
"multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
19+
"multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
20+
"fastqc_top_overrepresented_sequences_table.txt",
21+
"kallisto_alignment.txt",
22+
"multiqc_data.json",
23+
"multiqc_general_stats.txt",
24+
"multiqc_kallisto.txt",
25+
"multiqc_software_versions.txt",
26+
"multiqc_sources.txt"
27+
],
28+
"meta": {
29+
"nf-test": "0.9.0",
30+
"nextflow": "24.04.4"
31+
},
32+
"timestamp": "2024-08-23T15:53:37.272547"
33+
},
34+
"trimgalore": {
35+
"content": [
36+
"RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
37+
"RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
38+
"RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
39+
"RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
40+
"WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
41+
"WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
42+
"WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
43+
"WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
44+
],
45+
"meta": {
46+
"nf-test": "0.9.0",
47+
"nextflow": "24.04.4"
48+
},
49+
"timestamp": "2024-08-23T15:35:31.545385"
50+
},
51+
"kallisto": {
52+
"content": [
53+
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
54+
"abundance.h5",
55+
"abundance.tsv",
56+
"kallisto_quant.log",
57+
"run_info.json",
58+
"abundance.h5",
59+
"abundance.tsv",
60+
"kallisto_quant.log",
61+
"run_info.json",
62+
"abundance.h5",
63+
"abundance.tsv",
64+
"kallisto_quant.log",
65+
"run_info.json",
66+
"abundance.h5",
67+
"abundance.tsv",
68+
"kallisto_quant.log",
69+
"run_info.json",
70+
"abundance.h5",
71+
"abundance.tsv",
72+
"kallisto_quant.log",
73+
"run_info.json",
74+
"kallisto.merged.gene_counts.SummarizedExperiment.rds",
75+
"kallisto.merged.gene_counts.tsv",
76+
"kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds",
77+
"kallisto.merged.gene_counts_length_scaled.tsv",
78+
"kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds",
79+
"kallisto.merged.gene_counts_scaled.tsv",
80+
"kallisto.merged.gene_lengths.tsv",
81+
"kallisto.merged.gene_tpm.tsv",
82+
"kallisto.merged.transcript_counts.SummarizedExperiment.rds",
83+
"kallisto.merged.transcript_counts.tsv",
84+
"kallisto.merged.transcript_lengths.tsv",
85+
"kallisto.merged.transcript_tpm.tsv"
86+
],
87+
"meta": {
88+
"nf-test": "0.9.0",
89+
"nextflow": "24.04.4"
90+
},
91+
"timestamp": "2024-08-23T15:53:37.166056"
92+
},
93+
"references": {
94+
"content": [
95+
"genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
96+
"genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
97+
],
98+
"meta": {
99+
"nf-test": "0.9.0",
100+
"nextflow": "24.04.4"
101+
},
102+
"timestamp": "2024-08-23T15:25:12.683541"
103+
},
104+
"versions": {
105+
"content": [
106+
"{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}"
107+
],
108+
"meta": {
109+
"nf-test": "0.9.0",
110+
"nextflow": "24.04.4"
111+
},
112+
"timestamp": "2024-08-23T15:35:31.742801"
113+
},
114+
"fastqc/trim": {
115+
"content": [
116+
"RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html",
117+
"RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip",
118+
"RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html",
119+
"RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip",
120+
"RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html",
121+
"RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip",
122+
"RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html",
123+
"RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip",
124+
"WT_REP1_trimmed_1_val_1_fastqc.html",
125+
"WT_REP1_trimmed_1_val_1_fastqc.zip",
126+
"WT_REP1_trimmed_2_val_2_fastqc.html",
127+
"WT_REP1_trimmed_2_val_2_fastqc.zip",
128+
"WT_REP2_trimmed_1_val_1_fastqc.html",
129+
"WT_REP2_trimmed_1_val_1_fastqc.zip",
130+
"WT_REP2_trimmed_2_val_2_fastqc.html",
131+
"WT_REP2_trimmed_2_val_2_fastqc.zip"
132+
],
133+
"meta": {
134+
"nf-test": "0.9.0",
135+
"nextflow": "24.04.4"
136+
},
137+
"timestamp": "2024-08-23T15:25:12.695474"
138+
},
139+
"multiqc_plots": {
140+
"content": [
141+
"cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
142+
"cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
143+
"cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
144+
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
145+
"fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890",
146+
"fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f",
147+
"fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
148+
"fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959",
149+
"fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e",
150+
"fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
151+
"fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
152+
"fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
153+
"multiqc_report.html",
154+
"cutadapt_filtered_reads_plot-cnt.pdf",
155+
"cutadapt_filtered_reads_plot-pct.pdf",
156+
"cutadapt_trimmed_sequences_plot_3_Counts.pdf",
157+
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
158+
"fastqc-status-check-heatmap.pdf",
159+
"fastqc_overrepresented_sequences_plot.pdf",
160+
"fastqc_per_base_n_content_plot.pdf",
161+
"fastqc_per_base_sequence_quality_plot.pdf",
162+
"fastqc_per_sequence_gc_content_plot_Counts.pdf",
163+
"fastqc_per_sequence_gc_content_plot_Percentages.pdf",
164+
"fastqc_per_sequence_quality_scores_plot.pdf",
165+
"fastqc_sequence_counts_plot-cnt.pdf",
166+
"fastqc_sequence_counts_plot-pct.pdf",
167+
"fastqc_sequence_duplication_levels_plot.pdf",
168+
"fastqc_sequence_length_distribution_plot.pdf",
169+
"fastqc_top_overrepresented_sequences_table.pdf",
170+
"general_stats_table.pdf",
171+
"kallisto_alignment-cnt.pdf",
172+
"kallisto_alignment-pct.pdf",
173+
"fastqc_per_base_n_content_plot.png",
174+
"fastqc_per_base_sequence_quality_plot.png",
175+
"fastqc_sequence_length_distribution_plot.png",
176+
"fastqc_top_overrepresented_sequences_table.png",
177+
"general_stats_table.png",
178+
"kallisto_alignment-cnt.png",
179+
"kallisto_alignment-pct.png",
180+
"cutadapt_filtered_reads_plot-cnt.svg",
181+
"cutadapt_filtered_reads_plot-pct.svg",
182+
"cutadapt_trimmed_sequences_plot_3_Counts.svg",
183+
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
184+
"fastqc-status-check-heatmap.svg",
185+
"fastqc_overrepresented_sequences_plot.svg",
186+
"fastqc_per_base_n_content_plot.svg",
187+
"fastqc_per_base_sequence_quality_plot.svg",
188+
"fastqc_per_sequence_gc_content_plot_Counts.svg",
189+
"fastqc_per_sequence_gc_content_plot_Percentages.svg",
190+
"fastqc_per_sequence_quality_scores_plot.svg",
191+
"fastqc_sequence_counts_plot-cnt.svg",
192+
"fastqc_sequence_counts_plot-pct.svg",
193+
"fastqc_sequence_duplication_levels_plot.svg",
194+
"fastqc_sequence_length_distribution_plot.svg",
195+
"fastqc_top_overrepresented_sequences_table.svg",
196+
"general_stats_table.svg",
197+
"kallisto_alignment-cnt.svg",
198+
"kallisto_alignment-pct.svg"
199+
],
200+
"meta": {
201+
"nf-test": "0.9.0",
202+
"nextflow": "24.04.4"
203+
},
204+
"timestamp": "2024-08-23T15:53:37.413284"
205+
},
206+
"bbsplit": {
207+
"content": [
208+
"RAP1_IAA_30M_REP1.stats.txt",
209+
"RAP1_UNINDUCED_REP1.stats.txt",
210+
"RAP1_UNINDUCED_REP2.stats.txt",
211+
"WT_REP1.stats.txt",
212+
"WT_REP2.stats.txt"
213+
],
214+
"meta": {
215+
"nf-test": "0.9.0",
216+
"nextflow": "24.04.4"
217+
},
218+
"timestamp": "2024-08-23T15:25:12.672876"
219+
},
220+
"Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": {
221+
"content": [
222+
"{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}",
223+
"genome_transcriptome.fasta",
224+
"genome_transcriptome.gtf",
225+
"multiqc_report.html",
226+
"RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
227+
"RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
228+
"RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
229+
"RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
230+
"WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
231+
"WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
232+
"WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
233+
"WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
234+
],
235+
"meta": {
236+
"nf-test": "0.9.0",
237+
"nextflow": "24.04.4"
238+
},
239+
"timestamp": "2024-08-23T15:36:19.174739"
240+
}
241+
}

0 commit comments

Comments
 (0)