Skip to content

Commit 2439102

Browse files
RZ9082RZ9082
committed
Updated names and updated MultiQC version
1 parent 597ae96 commit 2439102

File tree

14 files changed

+1048
-1330
lines changed

14 files changed

+1048
-1330
lines changed

‎workflows/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2-tests.yml‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -38,16 +38,16 @@
3838
class: File
3939
location: https://zenodo.org/records/13347829/files/test_metadata_formatted.tabular
4040
outputs:
41-
OTU_table:
41+
OTU table:
4242
location: https://zenodo.org/records/13347829/files/OTU_table.tabular
43-
tax_table:
44-
location: https://zenodo.org/records/13347829/files/tax_table.tabular
45-
ampvis:
43+
Taxonomy table:
44+
location: https://zenodo.org/records/14745803/files/tax_table.tabular
45+
Ampvis2 object:
4646
asserts:
4747
- that: has_size
4848
value: 15000
4949
delta: 1000
50-
metadata_list_out:
50+
Ampvis2 metadata table:
5151
location: https://zenodo.org/records/13347829/files/metadata_list.tabular
52-
taxonomy_list_out:
53-
location: https://zenodo.org/records/13347829/files/taxonomy_list.tabular
52+
Ampvis2 taxonomy table:
53+
location: https://zenodo.org/records/14745803/files/taxonomy_list.tabular

‎workflows/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2.ga‎

Lines changed: 71 additions & 49 deletions
Large diffs are not rendered by default.

‎workflows/amplicon-mgnify/mgnify-amplicon-pipeline-v5-complete/mgnify-amplicon-pipeline-v5-complete-tests.yml‎

Lines changed: 51 additions & 71 deletions
Original file line numberDiff line numberDiff line change
@@ -7,41 +7,35 @@
77
class: File
88
location: "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/rfam_models/ribosomal_models/ribo.claninfo"
99
outputs:
10-
SE_MultiQC_report:
10+
Single-end MultiQC report:
1111
asserts:
1212
- that: has_text
1313
text: "DRR010481_ambiguous_base_filtering"
1414
- that: has_text
15-
text: "<span class=\"val\">84.0%</span>"
15+
text: "84.0"
1616
- that: has_text
1717
text: "DRR010481_initial_reads"
1818
- that: has_text
19-
text: "<span class=\"val\">84.8%</span>"
19+
text: "84.8"
2020
- that: has_text
2121
text: "DRR010481_length_filtering"
2222
- that: has_text
2323
text: "DRR010481_trimming"
24-
SE_QC_processed_FASTA:
24+
Single-end post quality control FASTA files:
2525
element_tests:
2626
DRR010481:
2727
location: https://zenodo.org/records/13710235/files/DRR010481_SE.fasta
28-
SE_MultiQC_stats:
29-
element_tests:
30-
fastqc:
31-
location: https://zenodo.org/records/14499545/files/fastqc_SE.tabular
32-
general_stats:
33-
location: https://zenodo.org/records/14499545/files/general_stats_SE.tabular
34-
sources:
35-
asserts:
36-
- that: has_text
37-
text: "FastQC all_sections DRR010481_ambiguous_base_filtering"
38-
- that: has_text
39-
text: "FastQC all_sections DRR010481_initial_reads"
40-
- that: has_text
41-
text: "FastQC all_sections DRR010481_length_filtering"
42-
- that: has_text
43-
text: "FastQC all_sections DRR010481_trimming"
44-
PE_MultiQC_report:
28+
Single-end MultiQC statistics:
29+
asserts:
30+
- that: has_text
31+
text: "DRR010481_ambiguous_base_filtering 84.0 47.0 242.02 244 40.0 2.4999999999999998e-05"
32+
- that: has_text
33+
text: "DRR010481_initial_reads 84.84848484848484 47.0 545.0454545454545 550 40.0 3.2999999999999996e-05"
34+
- that: has_text
35+
text: "DRR010481_length_filtering 84.0 47.0 242.02 244 40.0 2.4999999999999998e-05"
36+
- that: has_text
37+
text: "DRR010481_trimming 84.0 47.0 242.02 244 40.0 2.4999999999999998e-05"
38+
Paired-end MultiQC report:
4539
asserts:
4640
- that: has_text
4741
text: "ERR2715528_ambiguous_base_filtering"
@@ -52,33 +46,19 @@
5246
- that: has_text
5347
text: "ERR2715528_trimming"
5448
- that: has_text
55-
text: "<span class=\"val\">92.2%</span>"
56-
PE_MultiQC_stats:
57-
element_tests:
58-
fastqc:
59-
location: https://zenodo.org/records/13710235/files/fastqc_PE.tabular
60-
general_stats:
61-
location: https://zenodo.org/records/13710235/files/general_stats_PE.tabular
62-
sources:
63-
asserts:
64-
- that: has_text
65-
text: "FastQC all_sections ERR2715528_ambiguous_base_filtering"
66-
- that: has_text
67-
text: "FastQC all_sections ERR2715528_initial_reads"
68-
- that: has_text
69-
text: "FastQC all_sections ERR2715528_length_filtering"
70-
- that: has_text
71-
text: "FastQC all_sections ERR2715528_trimming"
72-
PE_QC_processed_FASTA:
49+
text: "92.2"
50+
Paired-end MultiQC statistics:
51+
location: https://zenodo.org/records/14746033/files/general_stats_PE.tabular
52+
Paired-end post quality control FASTA files:
7353
element_tests:
7454
ERR2715528:
7555
location: https://zenodo.org/records/13710235/files/ERR2715528_PE.fasta
76-
LSU_FASTA:
56+
LSU FASTA files:
7757
element_tests:
7858
DRR010481:
7959
location: https://zenodo.org/records/13710235/files/DRR010481_LSU.fasta
8060
compare: contains
81-
Classifications_SSU_SILVA:
61+
SSU taxonomic classifications using SILVA DB:
8262
element_tests:
8363
ERR2715528:
8464
asserts:
@@ -89,7 +69,7 @@
8969
- that: has_n_columns
9070
comment: "#"
9171
n: 15
92-
OTU_SSU_SILVA:
72+
SSU OTU tables (SILVA DB):
9373
element_tests:
9474
ERR2715528:
9575
asserts:
@@ -106,7 +86,7 @@
10686
- that: has_n_columns
10787
comment: "#"
10888
n: 4
109-
OTU_LSU_SILVA:
89+
LSU OTU tables (SILVA DB):
11090
element_tests:
11191
DRR010481:
11292
asserts:
@@ -123,41 +103,41 @@
123103
- that: has_n_columns
124104
comment: "#"
125105
n: 4
126-
HDF5_SSU_SILVA:
106+
SSU OTU tables in HDF5 format (SILVA DB):
127107
element_tests:
128108
ERR2715528:
129109
asserts:
130110
- that: has_size
131111
value: 37000
132112
delta: 10000
133-
JSON_SSU_SILVA:
113+
SSU OTU tables in JSON format (SILVA DB):
134114
element_tests:
135115
ERR2715528:
136116
asserts:
137117
- that: has_text
138118
text: "\"type\": \"OTU table\""
139-
Krona_SSU_SILVA:
119+
SSU taxonomic abundance pie charts (SILVA DB):
140120
asserts:
141121
- that: has_text
142122
text: "ERR2715528"
143-
HDF5_LSU_SILVA:
123+
LSU OTU tables in HDF5 format (SILVA DB):
144124
element_tests:
145125
DRR010481:
146126
asserts:
147127
- that: has_size
148128
value: 37000
149129
delta: 10000
150-
JSON_LSU_SILVA:
130+
LSU OTU tables in JSON format (SILVA DB):
151131
element_tests:
152132
DRR010481:
153133
asserts:
154134
- that: has_text
155135
text: "\"type\": \"OTU table\""
156-
Krona_LSU_SILVA:
136+
LSU taxonomic abundance pie charts (SILVA DB):
157137
asserts:
158138
- that: has_text
159139
text: "DRR010481"
160-
Classifications_LSU_SILVA:
140+
LSU taxonomic classifications using SILVA DB:
161141
element_tests:
162142
DRR010481:
163143
asserts:
@@ -168,18 +148,18 @@
168148
- that: has_n_columns
169149
comment: "#"
170150
n: 15
171-
SSU_FASTA:
151+
SSU FASTA files:
172152
element_tests:
173153
ERR2715528:
174154
location: https://zenodo.org/records/13710235/files/ERR2715528_SSU.fasta
175155
compare: contains
176-
LSU_SSU_BED:
156+
LSU and SSU BED regions:
177157
element_tests:
178158
DRR010481:
179159
location: https://zenodo.org/records/13710235/files/DRR010481.bed
180160
ERR2715528:
181161
location: https://zenodo.org/records/13710235/files/ERR2715528.bed
182-
Classifications_ITSoneDB:
162+
ITS taxonomic classifications using ITSoneDB:
183163
element_tests:
184164
DRR010481:
185165
asserts:
@@ -199,15 +179,15 @@
199179
- that: has_n_columns
200180
comment: "#"
201181
n: 15
202-
ITS_FASTA:
182+
ITS FASTA files:
203183
element_tests:
204184
DRR010481:
205185
location: https://zenodo.org/records/13710235/files/DRR010481_ITS.fasta
206186
compare: contains
207187
ERR2715528:
208188
location: https://zenodo.org/records/13710235/files/ERR2715528_ITS.fasta
209189
compare: contains
210-
JSON_ITS_UNITE:
190+
ITS OTU tables in JSON format (UNITE DB):
211191
element_tests:
212192
DRR010481:
213193
asserts:
@@ -217,13 +197,13 @@
217197
asserts:
218198
- that: has_text
219199
text: "\"type\": \"OTU table\""
220-
Krona_ITS_UNITE:
200+
ITS taxonomic abundance pie charts (UNITE DB):
221201
asserts:
222202
- that: has_text
223203
text: "DRR010481"
224204
- that: has_text
225205
text: "ERR2715528"
226-
HDF5_ITS_UNITE:
206+
ITS OTU tables in HDF5 format (UNITE DB):
227207
element_tests:
228208
DRR010481:
229209
asserts:
@@ -235,13 +215,13 @@
235215
- that: has_size
236216
value: 72000
237217
delta: 10000
238-
Krona_ITSoneDB:
218+
ITS taxonomic abundance pie charts (ITSoneDB):
239219
asserts:
240220
- that: has_text
241221
text: "DRR010481"
242222
- that: has_text
243223
text: "ERR2715528"
244-
JSON_ITSoneDB:
224+
ITS OTU tables in JSON format (ITSoneDB):
245225
element_tests:
246226
DRR010481:
247227
asserts:
@@ -251,7 +231,7 @@
251231
asserts:
252232
- that: has_text
253233
text: "\"type\": \"OTU table\""
254-
HDF5_ITSoneDB:
234+
ITS OTU tables in HDF5 format (ITSoneDB):
255235
element_tests:
256236
DRR010481:
257237
asserts:
@@ -263,7 +243,7 @@
263243
- that: has_size
264244
value: 72000
265245
delta: 10000
266-
Classifications_ITS_UNITE:
246+
ITS taxonomic classifications using UNITE DB:
267247
element_tests:
268248
DRR010481:
269249
asserts:
@@ -283,7 +263,7 @@
283263
- that: has_n_columns
284264
comment: "#"
285265
n: 15
286-
OTU_ITS_UNITE:
266+
ITS OTU tables (UNITE DB):
287267
element_tests:
288268
DRR010481:
289269
asserts:
@@ -315,7 +295,7 @@
315295
- that: has_n_columns
316296
comment: "#"
317297
n: 4
318-
OTU_ITSoneDB:
298+
ITS OTU tables (ITSoneDB):
319299
element_tests:
320300
DRR010481:
321301
asserts:
@@ -347,7 +327,7 @@
347327
- that: has_n_columns
348328
comment: "#"
349329
n: 4
350-
ITSoneDB_phylum_taxonomic_summary_table:
330+
ITSoneDB phylum level taxonomic abundance summary table:
351331
asserts:
352332
- that: has_text
353333
text: 'superkingdom kingdom phylum DRR010481 ERR2715528'
@@ -356,7 +336,7 @@
356336
- that: has_n_lines
357337
n: 10
358338
delta: 4
359-
ITSoneDB_taxonomic_summary_table:
339+
ITSoneDB taxonomic abundance summary table:
360340
asserts:
361341
- that: has_text
362342
text: '#SampleID DRR010481 ERR2715528'
@@ -365,7 +345,7 @@
365345
- that: has_n_lines
366346
n: 117
367347
delta: 17
368-
LSU_phylum_taxonomic_summary_table:
348+
LSU phylum level taxonomic abundance summary table:
369349
asserts:
370350
- that: has_text
371351
text: 'superkingdom kingdom phylum DRR010481'
@@ -374,7 +354,7 @@
374354
- that: has_n_lines
375355
n: 6
376356
delta: 4
377-
LSU_taxonomic_summary_table:
357+
LSU taxonomic abundance summary table:
378358
asserts:
379359
- that: has_text
380360
text: '#SampleID DRR010481'
@@ -383,7 +363,7 @@
383363
- that: has_n_lines
384364
n: 6
385365
delta: 4
386-
SSU_phylum_taxonomic_summary_table:
366+
SSU phylum level taxonomic abundance summary table:
387367
asserts:
388368
- that: has_text
389369
text: 'superkingdom kingdom phylum ERR2715528'
@@ -392,7 +372,7 @@
392372
- that: has_n_lines
393373
n: 12
394374
delta: 4
395-
SSU_taxonomic_summary_table:
375+
SSU taxonomic abundance summary table:
396376
asserts:
397377
- that: has_text
398378
text: '#SampleID ERR2715528'
@@ -401,7 +381,7 @@
401381
- that: has_n_lines
402382
n: 13
403383
delta: 4
404-
UNITE_phylum_taxonomic_summary_table:
384+
ITS UNITE DB phylum level taxonomic abundance summary table:
405385
asserts:
406386
- that: has_text
407387
text: 'superkingdom kingdom phylum DRR010481 ERR2715528'
@@ -410,7 +390,7 @@
410390
- that: has_n_lines
411391
n: 13
412392
delta: 4
413-
UNITE_taxonomic_summary_table:
393+
ITS UNITE DB taxonomic abundance summary table:
414394
asserts:
415395
- that: has_text
416396
text: '#SampleID DRR010481 ERR2715528'

0 commit comments

Comments
 (0)