Skip to content

Commit df1a244

Browse files
Aratznkongenellykedhammar
committed
Fix tests
Co-authored-by: nelnk861 <nelly.nkonge@uu.se> Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se>
1 parent d930935 commit df1a244

File tree

8 files changed

+139
-194
lines changed

8 files changed

+139
-194
lines changed

‎conf/modules.config‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ process {
3131
publishDir = [
3232
path: { "${params.outdir}/seqfu_stats" },
3333
mode: params.publish_dir_mode,
34-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
34+
saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.sample_id}_$filename" }
3535
]
3636
}
3737

‎tests/MiSeq.main.nf.test‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
11
nextflow_pipeline {
22

3-
name "Test Workflow main.nf on MiSeq data"
3+
name "Test Workflow main.nf on MiSeq data with single end reads"
44
script "../main.nf"
55
tag "seqinspector"
66
tag "PIPELINE"
77

8-
test("MiSeq data test") {
8+
test("MiSeq data test (single end reads)") {
99

1010
when {
1111
config "./MiSeq.main.nf.test.config"

‎tests/MiSeq.main.nf.test.snap‎

Lines changed: 54 additions & 54 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,36 @@
11
{
2-
"MiSeq data test": {
2+
"Miseq data test (skip all tools)": {
3+
"content": [
4+
1,
5+
{
6+
"Workflow": {
7+
"nf-core/seqinspector": "v1.0dev"
8+
}
9+
},
10+
[
11+
"multiqc",
12+
"multiqc/global_report",
13+
"multiqc/global_report/multiqc_data",
14+
"multiqc/global_report/multiqc_data/multiqc.log",
15+
"multiqc/global_report/multiqc_data/multiqc_citations.txt",
16+
"multiqc/global_report/multiqc_data/multiqc_data.json",
17+
"multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
18+
"multiqc/global_report/multiqc_data/multiqc_sources.txt",
19+
"multiqc/global_report/multiqc_report.html",
20+
"pipeline_info",
21+
"pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
22+
],
23+
[
24+
"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
25+
]
26+
],
27+
"meta": {
28+
"nf-test": "0.9.0",
29+
"nextflow": "24.10.3"
30+
},
31+
"timestamp": "2025-01-07T13:49:22.707398"
32+
},
33+
"MiSeq data test (single end reads)": {
334
"content": [
435
4,
536
{
@@ -39,17 +70,16 @@
3970
"multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
4071
"multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
4172
"multiqc/global_report/multiqc_data/multiqc.log",
42-
"multiqc/global_report/multiqc_data/multiqc_SAMPLE_SINGLE_END_1.txt",
4373
"multiqc/global_report/multiqc_data/multiqc_citations.txt",
4474
"multiqc/global_report/multiqc_data/multiqc_data.json",
4575
"multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
4676
"multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
4777
"multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
78+
"multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
4879
"multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
4980
"multiqc/global_report/multiqc_data/multiqc_sources.txt",
5081
"multiqc/global_report/multiqc_plots",
5182
"multiqc/global_report/multiqc_plots/pdf",
52-
"multiqc/global_report/multiqc_plots/pdf/SAMPLE_SINGLE_END_1.pdf",
5383
"multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
5484
"multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
5585
"multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
@@ -64,8 +94,8 @@
6494
"multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
6595
"multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
6696
"multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
97+
"multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
6798
"multiqc/global_report/multiqc_plots/png",
68-
"multiqc/global_report/multiqc_plots/png/SAMPLE_SINGLE_END_1.png",
6999
"multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
70100
"multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
71101
"multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
@@ -80,8 +110,8 @@
80110
"multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
81111
"multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
82112
"multiqc/global_report/multiqc_plots/png/general_stats_table.png",
113+
"multiqc/global_report/multiqc_plots/png/seqfu.png",
83114
"multiqc/global_report/multiqc_plots/svg",
84-
"multiqc/global_report/multiqc_plots/svg/SAMPLE_SINGLE_END_1.svg",
85115
"multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
86116
"multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
87117
"multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
@@ -96,12 +126,13 @@
96126
"multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
97127
"multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
98128
"multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
129+
"multiqc/global_report/multiqc_plots/svg/seqfu.svg",
99130
"multiqc/global_report/multiqc_report.html",
100131
"pipeline_info",
101132
"pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
102133
"seqfu_stats",
103-
"seqfu_stats/SAMPLE_SINGLE_END_1.tsv",
104-
"seqfu_stats/SAMPLE_SINGLE_END_1_mqc.txt"
134+
"seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
135+
"seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
105136
],
106137
[
107138
"SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
@@ -116,50 +147,19 @@
116147
"fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
117148
"fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
118149
"fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
119-
"multiqc_SAMPLE_SINGLE_END_1.txt:md5,8e6989a2392f599a09a5c3edf8119702",
120150
"multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
121151
"multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
122152
"multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
123-
"SAMPLE_SINGLE_END_1.tsv:md5,f65c868e562291647d539090698ba5eb",
124-
"SAMPLE_SINGLE_END_1_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
125-
]
126-
],
127-
"meta": {
128-
"nf-test": "0.9.0",
129-
"nextflow": "24.10.3"
130-
},
131-
"timestamp": "2025-02-04T10:07:47.514983"
132-
},
133-
"Miseq data test (skip all tools)": {
134-
"content": [
135-
1,
136-
{
137-
"Workflow": {
138-
"nf-core/seqinspector": "v1.0dev"
139-
}
140-
},
141-
[
142-
"multiqc",
143-
"multiqc/global_report",
144-
"multiqc/global_report/multiqc_data",
145-
"multiqc/global_report/multiqc_data/multiqc.log",
146-
"multiqc/global_report/multiqc_data/multiqc_citations.txt",
147-
"multiqc/global_report/multiqc_data/multiqc_data.json",
148-
"multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
149-
"multiqc/global_report/multiqc_data/multiqc_sources.txt",
150-
"multiqc/global_report/multiqc_report.html",
151-
"pipeline_info",
152-
"pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
153-
],
154-
[
155-
"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
153+
"multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
154+
"SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
155+
"SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
156156
]
157157
],
158158
"meta": {
159159
"nf-test": "0.9.0",
160-
"nextflow": "24.10.3"
160+
"nextflow": "24.10.4"
161161
},
162-
"timestamp": "2025-01-07T13:49:22.707398"
162+
"timestamp": "2025-03-26T13:00:21.042755"
163163
},
164164
"Miseq data test (skip fastqc)": {
165165
"content": [
@@ -185,47 +185,47 @@
185185
"multiqc/global_report/multiqc_data",
186186
"multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
187187
"multiqc/global_report/multiqc_data/multiqc.log",
188-
"multiqc/global_report/multiqc_data/multiqc_SAMPLE_SINGLE_END_1.txt",
189188
"multiqc/global_report/multiqc_data/multiqc_citations.txt",
190189
"multiqc/global_report/multiqc_data/multiqc_data.json",
191190
"multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
191+
"multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
192192
"multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
193193
"multiqc/global_report/multiqc_data/multiqc_sources.txt",
194194
"multiqc/global_report/multiqc_plots",
195195
"multiqc/global_report/multiqc_plots/pdf",
196-
"multiqc/global_report/multiqc_plots/pdf/SAMPLE_SINGLE_END_1.pdf",
197196
"multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
198197
"multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
198+
"multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
199199
"multiqc/global_report/multiqc_plots/png",
200-
"multiqc/global_report/multiqc_plots/png/SAMPLE_SINGLE_END_1.png",
201200
"multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
202201
"multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
202+
"multiqc/global_report/multiqc_plots/png/seqfu.png",
203203
"multiqc/global_report/multiqc_plots/svg",
204-
"multiqc/global_report/multiqc_plots/svg/SAMPLE_SINGLE_END_1.svg",
205204
"multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
206205
"multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
206+
"multiqc/global_report/multiqc_plots/svg/seqfu.svg",
207207
"multiqc/global_report/multiqc_report.html",
208208
"pipeline_info",
209209
"pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
210210
"seqfu_stats",
211-
"seqfu_stats/SAMPLE_SINGLE_END_1.tsv",
212-
"seqfu_stats/SAMPLE_SINGLE_END_1_mqc.txt"
211+
"seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
212+
"seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
213213
],
214214
[
215215
"SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
216216
"SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
217217
"fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
218-
"multiqc_SAMPLE_SINGLE_END_1.txt:md5,8e6989a2392f599a09a5c3edf8119702",
219218
"multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
220219
"multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
221-
"SAMPLE_SINGLE_END_1.tsv:md5,f65c868e562291647d539090698ba5eb",
222-
"SAMPLE_SINGLE_END_1_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
220+
"multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
221+
"SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
222+
"SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
223223
]
224224
],
225225
"meta": {
226226
"nf-test": "0.9.0",
227-
"nextflow": "24.10.3"
227+
"nextflow": "24.10.4"
228228
},
229-
"timestamp": "2025-02-03T16:40:27.8664"
229+
"timestamp": "2025-03-26T13:00:53.07934"
230230
}
231231
}

‎tests/MiSeq_PairedEnd.main.nf.test‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
11
nextflow_pipeline {
22

3-
name "Test Workflow main.nf on MiSeq data"
3+
name "Test Workflow main.nf on MiSeq data with paired end reads"
44
script "../main.nf"
55
tag "seqinspector"
66
tag "PIPELINE"
77

8-
test("MiSeq data test") {
8+
test("MiSeq data test (paired end reads)") {
99

1010
when {
1111
config "./MiSeq_PairedEnd.main.nf.test.config"

0 commit comments

Comments
 (0)