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Merge pull request #1016 from mvdbeek/add_hashes_to_most_workflow_test_inputs
Add hashes to most workflow tests
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‎workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml‎

Lines changed: 99 additions & 57 deletions
Original file line numberDiff line numberDiff line change
@@ -6,47 +6,65 @@
66
class: Collection
77
collection_type: list:paired
88
elements:
9-
- class: Collection
10-
type: paired
11-
identifier: Hi-C reads
12-
elements:
13-
- identifier: forward
14-
class: File
15-
location: https://zenodo.org/records/10068595/files/HiC%20forward%20reads.fastqsanger.gz?download=1
16-
filetype: fastqsanger.gz
17-
- identifier: reverse
18-
class: File
19-
location: https://zenodo.org/records/10068595/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
20-
filetype: fastqsanger.gz
9+
- class: Collection
10+
type: paired
11+
identifier: Hi-C reads
12+
elements:
13+
- identifier: forward
14+
class: File
15+
location: https://zenodo.org/records/10068595/files/HiC%20forward%20reads.fastqsanger.gz?download=1
16+
filetype: fastqsanger.gz
17+
hashes:
18+
- hash_function: SHA-1
19+
hash_value: eb2e87b12418c0665f5de6d97101a4fc088f8bdf
20+
- identifier: reverse
21+
class: File
22+
location: https://zenodo.org/records/10068595/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
23+
filetype: fastqsanger.gz
24+
hashes:
25+
- hash_function: SHA-1
26+
hash_value: 538110c9b14a5b11088a6999244ee04983389d80
2127
Genomescope Model Parameters:
2228
class: File
2329
path: test-data/Genomescope Model Parameters.tabular
2430
filetype: tabular
31+
hashes:
32+
- hash_function: SHA-1
33+
hash_value: 6daf4567ff37e9d5ceebf76ddeb15e0d5773f694
2534
Genomescope Summary:
2635
class: File
2736
location: https://zenodo.org/records/10068595/files/Genomescope%20Summary.txt?download=1
2837
filetype: txt
38+
hashes:
39+
- hash_function: SHA-1
40+
hash_value: 42c6e189d26791e637dbaee533ad13cab39a7c1b
2941
Meryl Database:
3042
class: File
3143
location: https://zenodo.org/records/10068595/files/Meryl%20Database.meryldb?download=1
3244
filetype: meryldb
45+
hashes:
46+
- hash_function: SHA-1
47+
hash_value: 95615073e670e81ca03e6582b7da437c915cfccd
3348
Pacbio Reads:
3449
class: Collection
3550
collection_type: list
3651
elements:
3752
- class: File
3853
identifier: yeast_reads_sub1.fastq.gz
3954
location: https://zenodo.org/records/10068595/files/Pacbio%20Reads%20Collection_yeast_reads_sub1.fastq.gz.fastq.gz?download=1
55+
hashes:
56+
- hash_function: SHA-1
57+
hash_value: 6757ca53673956e3f536d8f3fe08c6b3c6287d37
4058
Lineage: vertebrata_odb10
4159
Bits for bloom filter: 32
4260
Name for Haplotype 1: Hap1
4361
Name for Haplotype 2: Hap2
44-
Homozygous Read Coverage: null
62+
Homozygous Read Coverage:
4563
Database for Busco Lineage: v5
4664
Trim Hi-C reads?: false
4765
outputs:
4866
Hifiasm Hi-C hap1:
49-
asserts:
67+
asserts:
5068
has_n_lines:
5169
n: 114
5270
Estimated Genome size: 2288021
@@ -56,31 +74,31 @@
5674
value: 65000
5775
delta: 10000
5876
usable hap1 gfa:
59-
asserts:
77+
asserts:
6078
has_n_lines:
6179
n: 119
6280
No Sequences hap2 gfa:
6381
asserts:
6482
has_text:
65-
text: "S h2tg000001l * LN:i:43860 LN:i:43860 rd:i:45"
83+
text: "S\th2tg000001l\t*\tLN:i:43860\tLN:i:43860\trd:i:45"
6684
Assembly statistics for Hap1 and Hap2:
6785
asserts:
68-
has_text:
69-
text: "# scaffolds 57 51"
86+
has_text:
87+
text: "# scaffolds\t57\t51"
7088
Compleasm on Contigs hap1 Full Table:
71-
asserts:
89+
asserts:
7290
has_n_lines:
7391
n: 3356
7492
Compleasm on Contigs hap1 Translated Proteins:
75-
asserts:
93+
asserts:
7694
has_n_lines:
7795
n: 31142
7896
Compleasm on Contigs hap2 Full Table:
79-
asserts:
97+
asserts:
8098
has_n_lines:
8199
n: 3356
82100
Compleasm on Contigs hap2 Translated Proteins:
83-
asserts:
101+
asserts:
84102
has_n_lines:
85103
n: 23694
86104
Compleasm on Contigs hap1 Summary:
@@ -99,59 +117,83 @@
99117
class: Collection
100118
collection_type: list:paired
101119
elements:
102-
- class: Collection
103-
type: paired
104-
identifier: Hi-C reads 1
105-
elements:
106-
- identifier: forward
107-
class: File
108-
location: https://zenodo.org/records/10068595/files/HiC%20forward%20reads.fastqsanger.gz?download=1
109-
filetype: fastqsanger.gz
110-
- identifier: reverse
111-
class: File
112-
location: https://zenodo.org/records/10068595/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
113-
filetype: fastqsanger.gz
114-
- class: Collection
115-
type: paired
116-
identifier: Hi-C reads 2
117-
elements:
118-
- identifier: forward
119-
class: File
120-
location: https://zenodo.org/records/10068595/files/HiC%20forward%20reads.fastqsanger.gz?download=1
121-
filetype: fastqsanger.gz
122-
- identifier: reverse
123-
class: File
124-
location: https://zenodo.org/records/10068595/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
125-
filetype: fastqsanger.gz
120+
- class: Collection
121+
type: paired
122+
identifier: Hi-C reads 1
123+
elements:
124+
- identifier: forward
125+
class: File
126+
location: https://zenodo.org/records/10068595/files/HiC%20forward%20reads.fastqsanger.gz?download=1
127+
filetype: fastqsanger.gz
128+
hashes:
129+
- hash_function: SHA-1
130+
hash_value: eb2e87b12418c0665f5de6d97101a4fc088f8bdf
131+
- identifier: reverse
132+
class: File
133+
location: https://zenodo.org/records/10068595/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
134+
filetype: fastqsanger.gz
135+
hashes:
136+
- hash_function: SHA-1
137+
hash_value: 538110c9b14a5b11088a6999244ee04983389d80
138+
- class: Collection
139+
type: paired
140+
identifier: Hi-C reads 2
141+
elements:
142+
- identifier: forward
143+
class: File
144+
location: https://zenodo.org/records/10068595/files/HiC%20forward%20reads.fastqsanger.gz?download=1
145+
filetype: fastqsanger.gz
146+
hashes:
147+
- hash_function: SHA-1
148+
hash_value: eb2e87b12418c0665f5de6d97101a4fc088f8bdf
149+
- identifier: reverse
150+
class: File
151+
location: https://zenodo.org/records/10068595/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
152+
filetype: fastqsanger.gz
153+
hashes:
154+
- hash_function: SHA-1
155+
hash_value: 538110c9b14a5b11088a6999244ee04983389d80
126156
Genomescope Model Parameters:
127157
class: File
128158
path: test-data/Genomescope Model Parameters.tabular
129159
filetype: tabular
160+
hashes:
161+
- hash_function: SHA-1
162+
hash_value: 6daf4567ff37e9d5ceebf76ddeb15e0d5773f694
130163
Genomescope Summary:
131164
class: File
132165
location: https://zenodo.org/records/10068595/files/Genomescope%20Summary.txt?download=1
133166
filetype: txt
167+
hashes:
168+
- hash_function: SHA-1
169+
hash_value: 42c6e189d26791e637dbaee533ad13cab39a7c1b
134170
Meryl Database:
135171
class: File
136172
location: https://zenodo.org/records/10068595/files/Meryl%20Database.meryldb?download=1
137173
filetype: meryldb
174+
hashes:
175+
- hash_function: SHA-1
176+
hash_value: 95615073e670e81ca03e6582b7da437c915cfccd
138177
Pacbio Reads:
139178
class: Collection
140179
collection_type: list
141180
elements:
142181
- class: File
143182
identifier: yeast_reads_sub1.fastq.gz
144183
location: https://zenodo.org/records/10068595/files/Pacbio%20Reads%20Collection_yeast_reads_sub1.fastq.gz.fastq.gz?download=1
184+
hashes:
185+
- hash_function: SHA-1
186+
hash_value: 6757ca53673956e3f536d8f3fe08c6b3c6287d37
145187
Lineage: vertebrata_odb10
146188
Bits for bloom filter: 32
147189
Name for Haplotype 1: Hap1
148190
Name for Haplotype 2: Hap2
149-
Homozygous Read Coverage: null
191+
Homozygous Read Coverage:
150192
Database for Busco Lineage: v5
151193
Trim Hi-C reads?: false
152194
outputs:
153195
Hifiasm Hi-C hap1:
154-
asserts:
196+
asserts:
155197
has_n_lines:
156198
n: 114
157199
Estimated Genome size: 2288021
@@ -161,31 +203,31 @@
161203
value: 65000
162204
delta: 10000
163205
usable hap1 gfa:
164-
asserts:
206+
asserts:
165207
has_n_lines:
166208
n: 119
167209
No Sequences hap2 gfa:
168210
asserts:
169211
has_text:
170-
text: "S h2tg000001l * LN:i:43860 LN:i:43860 rd:i:45"
212+
text: "S\th2tg000001l\t*\tLN:i:43860\tLN:i:43860\trd:i:45"
171213
Assembly statistics for Hap1 and Hap2:
172214
asserts:
173-
has_text:
174-
text: "# scaffolds 57 51"
215+
has_text:
216+
text: "# scaffolds\t57\t51"
175217
Compleasm on Contigs hap1 Full Table:
176-
asserts:
218+
asserts:
177219
has_n_lines:
178220
n: 3356
179221
Compleasm on Contigs hap1 Translated Proteins:
180-
asserts:
222+
asserts:
181223
has_n_lines:
182224
n: 31142
183225
Compleasm on Contigs hap2 Full Table:
184-
asserts:
226+
asserts:
185227
has_n_lines:
186228
n: 3356
187229
Compleasm on Contigs hap2 Translated Proteins:
188-
asserts:
230+
asserts:
189231
has_n_lines:
190232
n: 23694
191233
Compleasm on Contigs hap1 Summary:
@@ -195,4 +237,4 @@
195237
Compleasm on Contigs hap2 Summary:
196238
asserts:
197239
has_text:
198-
text: "S:0.60%, 20"
240+
text: "S:0.60%, 20"

‎workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml‎

Lines changed: 36 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -6,61 +6,91 @@
66
class: File
77
location: https://zenodo.org/records/10056319/files/Meryl%20Database%20-%20Child.meryldb?download=1
88
filetype: meryldb
9+
hashes:
10+
- hash_function: SHA-1
11+
hash_value: d947eb6b317fcd30bc18e59f1ddd0afa52f72587
912
'Hapmer Database: Paternal':
1013
class: File
1114
location: https://zenodo.org/records/10056319/files/Hapmer%20Database%20-%20Paternal.meryldb?download=1
1215
filetype: meryldb
16+
hashes:
17+
- hash_function: SHA-1
18+
hash_value: cb3b00cbd6415c46ce2e4dc2d8a9f2430818a3ab
1319
'Hapmer Database: Maternal':
1420
class: File
1521
location: https://zenodo.org/records/10056319/files/Hapmer%20Database%20-%20Maternal.meryldb?download=1
1622
filetype: meryldb
23+
hashes:
24+
- hash_function: SHA-1
25+
hash_value: 2fca1ca9b87ad48c7f1291bac29abd98eb5f43d8
1726
Genomescope Summary:
1827
class: File
1928
location: https://zenodo.org/records/10056319/files/Genomescope%20Summary.txt?download=1
2029
filetype: txt
30+
hashes:
31+
- hash_function: SHA-1
32+
hash_value: c3614564b2c84ef811c5d8bc56c394624d283fe4
2133
Genomescope Model Parameters:
2234
class: File
2335
path: test-data/GenomeScope_Model_parameters.tabular
2436
filetype: tabular
37+
hashes:
38+
- hash_function: SHA-1
39+
hash_value: 6daf4567ff37e9d5ceebf76ddeb15e0d5773f694
2540
'Pacbio Reads Collection: child':
2641
class: Collection
2742
collection_type: list
2843
elements:
2944
- class: File
3045
identifier: yeast_reads_sub1.fastq.gz
3146
location: https://zenodo.org/records/10056319/files/Pacbio%20Reads%20Collection.fastq.gz?download=1
47+
hashes:
48+
- hash_function: SHA-1
49+
hash_value: 6757ca53673956e3f536d8f3fe08c6b3c6287d37
3250
Paternal Illumina reads (hap1):
3351
class: Collection
3452
collection_type: list
3553
elements:
3654
- class: File
3755
identifier: hap1_2.fq
3856
location: https://zenodo.org/records/10056319/files/Sub_hap1_2.fastqsanger?download=1
57+
hashes:
58+
- hash_function: SHA-1
59+
hash_value: dccc29434921e0ac1b22819a2bc39c1a293f4f4a
3960
- class: File
4061
identifier: hap1_1.fq
4162
location: https://zenodo.org/records/10056319/files/Sub_hap1_1.fastqsanger?download=1
63+
hashes:
64+
- hash_function: SHA-1
65+
hash_value: 18776ce58066ec81ec47cf5a9987a5f3ba911348
4266
Maternal Illumina reads (hap2):
4367
class: Collection
4468
collection_type: list
4569
elements:
4670
- class: File
4771
identifier: hap2_2.fq
4872
location: https://zenodo.org/records/10056319/files/Sub_hap2_2.fastqsanger?download=1
73+
hashes:
74+
- hash_function: SHA-1
75+
hash_value: dc93abf6733d6069c7fc5c1d250527844638a91c
4976
- class: File
5077
identifier: hap2_1.fq
5178
location: https://zenodo.org/records/10056319/files/Sub_hap2_1.fastqsanger?download=1
52-
Homozygous Read Coverage: null
79+
hashes:
80+
- hash_function: SHA-1
81+
hash_value: 450db0747f0d09b18e6b9c16b4d1aef8243bfa24
82+
Homozygous Read Coverage:
5383
Bits for bloom filter: 32
5484
Name for Haplotype 1: Hap1
5585
Name for Haplotype 2: Hap2
5686
Database for Busco Lineage: v5
57-
Lineage: vertebrata_odb10
87+
Lineage: vertebrata_odb10
5888
outputs:
59-
Estimated Genome size: 2288021
89+
Estimated Genome size: 2288021
6090
Assembly statistics for Hap1 and Hap2:
6191
asserts:
6292
has_line:
63-
line: "# contigs 81 27"
93+
line: "# contigs\t81\t27"
6494
usable hap1 gfa:
6595
asserts:
6696
has_n_lines:
@@ -75,7 +105,7 @@
75105
text: "C:1.2%[S:1.1%,D:0.0%],F:0.4%,M:98.4%"
76106
Nx Plot:
77107
asserts:
78-
has_size:
108+
has_size:
79109
value: 65000
80110
delta: 5000
81111
No Sequence hap1 gfa:
@@ -89,4 +119,4 @@
89119
"Compleasm on Hap2 (maternal) contigs: Translated Proteins":
90120
asserts:
91121
has_n_lines:
92-
n: 13376
122+
n: 13376

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