Skip to content

Commit 39a0053

Browse files
chore: Merge branch 'dev-sovacool' of https://github.com/NIDAP-Community/MOSuite-CodeOcean into dev-sovacool
2 parents 711b38a + 5cba72d commit 39a0053

4 files changed

Lines changed: 342 additions & 72 deletions

File tree

.codeocean/app-panel.json

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,10 @@
11
{
22
"version": 1,
33
"processes": [
4-
"capsule_mosuite_clean_1",
5-
"capsule_mosuite_create_2"
4+
"capsule_mosuite_create_multiomicdataset_4",
5+
"capsule_mosuite_clean_raw_counts_5",
6+
"capsule_mosuite_filter_low_counts_6",
7+
"capsule_mosuite_normalize_counts_7",
8+
"capsule_mosuite_batch_correct_counts_8"
69
]
710
}

.codeocean/nextflow.json

Lines changed: 91 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -2,37 +2,59 @@
22
"version": 2,
33
"processes": [
44
{
5-
"name": "capsule_mosuite_clean_1",
5+
"name": "capsule_mosuite_create_multiomicdataset_4",
6+
"capsule": {
7+
"id": "5ce5f88d-980d-4e61-b3a4-ef4a0ce48030",
8+
"name": "MOSuite - create multiOmicDataSet",
9+
"slug": "6541445",
10+
"version": 5,
11+
"app_panel": true
12+
},
13+
"resources": {
14+
"cpus": 1,
15+
"memory": 8
16+
},
17+
"inputs": [
18+
{
19+
"id": "2QoMEOBD6Wkh3DWm",
20+
"source_id": "bd9a7518-66cb-4d50-9992-df3271aeb807",
21+
"type": "dataset",
22+
"name": "nidap-1.0",
23+
"source_path": "nidap-1.0/",
24+
"collect": true
25+
}
26+
]
27+
},
28+
{
29+
"name": "capsule_mosuite_clean_raw_counts_5",
630
"capsule": {
731
"id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b",
8-
"name": "MOSuite-clean",
32+
"name": "MOSuite - clean raw counts",
933
"slug": "5801113",
10-
"version": 2,
34+
"version": 3,
1135
"app_panel": true
1236
},
1337
"resources": {
1438
"cpus": 1,
15-
"memory": 4
39+
"memory": 8
1640
},
1741
"inputs": [
1842
{
19-
"id": "2P0EuEmZ9xTRXDi4",
20-
"source_id": "capsule_mosuite_create_2",
43+
"id": "MpqDzOmjzI6k7acV",
44+
"source_id": "capsule_mosuite_create_multiomicdataset_4",
2145
"type": "capsule",
22-
"name": "MOSuite-create"
46+
"name": "MOSuite-create",
47+
"collect": true
2348
}
24-
],
25-
"results": {
26-
"id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b"
27-
}
49+
]
2850
},
2951
{
30-
"name": "capsule_mosuite_create_2",
52+
"name": "capsule_mosuite_filter_low_counts_6",
3153
"capsule": {
32-
"id": "5ce5f88d-980d-4e61-b3a4-ef4a0ce48030",
33-
"name": "MOSuite-create",
34-
"slug": "6541445",
35-
"version": 4,
54+
"id": "0296f612-3498-4ed0-ac13-50620e45d67d",
55+
"name": "MOSuite - filter low counts",
56+
"slug": "4565215",
57+
"version": 1,
3658
"app_panel": true
3759
},
3860
"resources": {
@@ -41,14 +63,62 @@
4163
},
4264
"inputs": [
4365
{
44-
"id": "0EPP5jk5bdTFG7OY",
45-
"source_id": "bd9a7518-66cb-4d50-9992-df3271aeb807",
46-
"type": "dataset",
47-
"name": "nidap-1.0",
48-
"source_path": "nidap-1.0/",
66+
"id": "5mMm7tSyL4NR9Kfo",
67+
"source_id": "capsule_mosuite_clean_raw_counts_5",
68+
"type": "capsule",
69+
"name": "MOSuite-clean",
4970
"collect": true
5071
}
5172
]
73+
},
74+
{
75+
"name": "capsule_mosuite_normalize_counts_7",
76+
"capsule": {
77+
"id": "75561d95-aa78-4140-b64d-ddae5b64fc39",
78+
"name": "MOSuite - normalize counts",
79+
"slug": "9169525",
80+
"version": 1,
81+
"app_panel": true
82+
},
83+
"resources": {
84+
"cpus": 1,
85+
"memory": 8
86+
},
87+
"inputs": [
88+
{
89+
"id": "QU4dCV5IbfyyUbob",
90+
"source_id": "capsule_mosuite_filter_low_counts_6",
91+
"type": "capsule",
92+
"name": "MOSuite - filter low counts",
93+
"collect": true
94+
}
95+
]
96+
},
97+
{
98+
"name": "capsule_mosuite_batch_correct_counts_8",
99+
"capsule": {
100+
"id": "065804a2-efa7-43f2-9692-967bf0d6b592",
101+
"name": "MOSuite - batch correct counts",
102+
"slug": "1373453",
103+
"version": 1,
104+
"app_panel": true
105+
},
106+
"resources": {
107+
"cpus": 1,
108+
"memory": 8
109+
},
110+
"inputs": [
111+
{
112+
"id": "0RTvklzjFbQIkCtU",
113+
"source_id": "capsule_mosuite_normalize_counts_7",
114+
"type": "capsule",
115+
"name": "MOSuite - normalize counts",
116+
"collect": true
117+
}
118+
],
119+
"results": {
120+
"id": "2eae5a71-36a6-44e2-a3b2-2cd5634b445d"
121+
}
52122
}
53123
]
54124
}

.codeocean/pipeline-layout.json

Lines changed: 86 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -1,69 +1,125 @@
11
{
22
"edges": [
33
{
4-
"id": "xy-edge__capsule_mosuite_clean_1-results",
5-
"source": "capsule_mosuite_clean_1",
6-
"target": "results"
4+
"id": "xy-edge__bd9a7518-66cb-4d50-9992-df3271aeb807-capsule_mosuite_create_multiomicdataset_4",
5+
"selected": false,
6+
"source": "bd9a7518-66cb-4d50-9992-df3271aeb807",
7+
"target": "capsule_mosuite_create_multiomicdataset_4"
78
},
89
{
9-
"id": "xy-edge__capsule_mosuite_create_2-capsule_mosuite_clean_1",
10-
"source": "capsule_mosuite_create_2",
11-
"target": "capsule_mosuite_clean_1"
10+
"id": "xy-edge__capsule_mosuite_create_multiomicdataset_4-capsule_mosuite_clean_raw_counts_5",
11+
"selected": false,
12+
"source": "capsule_mosuite_create_multiomicdataset_4",
13+
"target": "capsule_mosuite_clean_raw_counts_5"
1214
},
1315
{
14-
"id": "xy-edge__bd9a7518-66cb-4d50-9992-df3271aeb807-capsule_mosuite_create_2",
15-
"source": "bd9a7518-66cb-4d50-9992-df3271aeb807",
16-
"target": "capsule_mosuite_create_2"
16+
"id": "xy-edge__capsule_mosuite_clean_raw_counts_5-capsule_mosuite_filter_low_counts_6",
17+
"selected": false,
18+
"source": "capsule_mosuite_clean_raw_counts_5",
19+
"target": "capsule_mosuite_filter_low_counts_6"
20+
},
21+
{
22+
"id": "xy-edge__capsule_mosuite_filter_low_counts_6-capsule_mosuite_normalize_counts_7",
23+
"selected": false,
24+
"source": "capsule_mosuite_filter_low_counts_6",
25+
"target": "capsule_mosuite_normalize_counts_7"
26+
},
27+
{
28+
"id": "xy-edge__capsule_mosuite_normalize_counts_7-capsule_mosuite_batch_correct_counts_8",
29+
"selected": false,
30+
"source": "capsule_mosuite_normalize_counts_7",
31+
"target": "capsule_mosuite_batch_correct_counts_8"
32+
},
33+
{
34+
"id": "xy-edge__capsule_mosuite_batch_correct_counts_8-results",
35+
"source": "capsule_mosuite_batch_correct_counts_8",
36+
"target": "results"
1737
}
1838
],
1939
"nodes": [
40+
{
41+
"id": "results",
42+
"position": {
43+
"x": 1303.2016865226233,
44+
"y": 978.5350198559569
45+
},
46+
"selected": false,
47+
"type": "results"
48+
},
49+
{
50+
"id": "bd9a7518-66cb-4d50-9992-df3271aeb807",
51+
"position": {
52+
"x": 803.9578354285136,
53+
"y": -268.2178495330654
54+
},
55+
"selected": false,
56+
"type": "dataset"
57+
},
2058
{
2159
"data": {
22-
"capsule_id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b"
60+
"capsule_id": "5ce5f88d-980d-4e61-b3a4-ef4a0ce48030"
2361
},
24-
"id": "capsule_mosuite_clean_1",
62+
"id": "capsule_mosuite_create_multiomicdataset_4",
2563
"position": {
26-
"x": 842.6666666666667,
27-
"y": 270
64+
"x": 863.0161630104416,
65+
"y": -140.81658464109762
2866
},
2967
"selected": false,
3068
"type": "capsule"
3169
},
3270
{
33-
"id": "results",
71+
"data": {
72+
"capsule_id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b"
73+
},
74+
"id": "capsule_mosuite_clean_raw_counts_5",
3475
"position": {
35-
"x": 1017.3333333333334,
36-
"y": 560.6666666666666
76+
"x": 914.6666666666667,
77+
"y": 62
3778
},
38-
"selected": true,
39-
"type": "results"
79+
"selected": false,
80+
"type": "capsule"
4081
},
4182
{
4283
"data": {
43-
"capsule_id": "5ce5f88d-980d-4e61-b3a4-ef4a0ce48030"
84+
"capsule_id": "0296f612-3498-4ed0-ac13-50620e45d67d"
4485
},
45-
"id": "capsule_mosuite_create_2",
86+
"id": "capsule_mosuite_filter_low_counts_6",
4687
"position": {
47-
"x": 709.3333333333333,
48-
"y": 39.33333333333334
88+
"x": 1009.7465449291838,
89+
"y": 263.6041227781795
4990
},
5091
"selected": false,
5192
"type": "capsule"
5293
},
5394
{
54-
"id": "bd9a7518-66cb-4d50-9992-df3271aeb807",
95+
"data": {
96+
"capsule_id": "75561d95-aa78-4140-b64d-ddae5b64fc39"
97+
},
98+
"id": "capsule_mosuite_normalize_counts_7",
5599
"position": {
56-
"x": 603.9999999999999,
57-
"y": -144.66666666666666
100+
"x": 1066.5598500534134,
101+
"y": 506.34949634377494
58102
},
59103
"selected": false,
60-
"type": "dataset"
104+
"type": "capsule"
105+
},
106+
{
107+
"data": {
108+
"capsule_id": "065804a2-efa7-43f2-9692-967bf0d6b592"
109+
},
110+
"id": "capsule_mosuite_batch_correct_counts_8",
111+
"position": {
112+
"x": 1216.1218082601067,
113+
"y": 719.312719442436
114+
},
115+
"selected": true,
116+
"type": "capsule"
61117
}
62118
],
63-
"timestamp": 1769627284612,
119+
"timestamp": 1769728345803,
64120
"viewport": {
65-
"x": -104,
66-
"y": 248,
67-
"zoom": 0.75
121+
"x": -233.0726228878891,
122+
"y": 188.02939462554733,
123+
"zoom": 0.6151296833975448
68124
}
69125
}

0 commit comments

Comments
 (0)