Skip to content

Commit 0c3143e

Browse files
kelly-sovacoolkelly-sovacool
committed
chore: update capsule versions
1 parent b7f526c commit 0c3143e

5 files changed

Lines changed: 52 additions & 25 deletions

File tree

‎.codeocean/app-panel.json‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
{
22
"version": 1,
33
"processes": [
4-
"capsule_mosuite_create_2",
5-
"capsule_mosuite_clean_1"
4+
"capsule_mosuite_clean_1",
5+
"capsule_mosuite_create_2"
66
]
77
}

‎.codeocean/datasets.json‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,8 @@
22
"version": 1,
33
"attached_datasets": [
44
{
5-
"id": "4ea90259-b1ac-491b-8571-5c25a8a98529",
6-
"mount": "moo-create"
5+
"id": "bd9a7518-66cb-4d50-9992-df3271aeb807",
6+
"mount": "nidap-1.0"
77
}
88
]
99
}

‎.codeocean/nextflow.json‎

Lines changed: 14 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -12,11 +12,11 @@
1212
},
1313
"resources": {
1414
"cpus": 1,
15-
"memory": 8
15+
"memory": 4
1616
},
1717
"inputs": [
1818
{
19-
"id": "NLgJ8e32jH3YibWL",
19+
"id": "2P0EuEmZ9xTRXDi4",
2020
"source_id": "capsule_mosuite_create_2",
2121
"type": "capsule",
2222
"name": "MOSuite-create"
@@ -32,13 +32,23 @@
3232
"id": "5ce5f88d-980d-4e61-b3a4-ef4a0ce48030",
3333
"name": "MOSuite-create",
3434
"slug": "6541445",
35-
"version": 3,
35+
"version": 4,
3636
"app_panel": true
3737
},
3838
"resources": {
3939
"cpus": 1,
4040
"memory": 8
41-
}
41+
},
42+
"inputs": [
43+
{
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/",
49+
"collect": true
50+
}
51+
]
4252
}
4353
]
4454
}

‎.codeocean/pipeline-layout.json‎

Lines changed: 26 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,19 @@
11
{
22
"edges": [
3+
{
4+
"id": "xy-edge__capsule_mosuite_clean_1-results",
5+
"source": "capsule_mosuite_clean_1",
6+
"target": "results"
7+
},
38
{
49
"id": "xy-edge__capsule_mosuite_create_2-capsule_mosuite_clean_1",
510
"source": "capsule_mosuite_create_2",
611
"target": "capsule_mosuite_clean_1"
712
},
813
{
9-
"id": "xy-edge__capsule_mosuite_clean_1-results",
10-
"source": "capsule_mosuite_clean_1",
11-
"target": "results"
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"
1217
}
1318
],
1419
"nodes": [
@@ -21,15 +26,16 @@
2126
"x": 842.6666666666667,
2227
"y": 270
2328
},
24-
"selected": true,
29+
"selected": false,
2530
"type": "capsule"
2631
},
2732
{
2833
"id": "results",
2934
"position": {
30-
"x": 960,
31-
"y": 614
35+
"x": 1017.3333333333334,
36+
"y": 560.6666666666666
3237
},
38+
"selected": true,
3339
"type": "results"
3440
},
3541
{
@@ -38,17 +44,26 @@
3844
},
3945
"id": "capsule_mosuite_create_2",
4046
"position": {
41-
"x": 718.6666666666666,
42-
"y": 31.333333333333343
47+
"x": 709.3333333333333,
48+
"y": 39.33333333333334
4349
},
4450
"selected": false,
4551
"type": "capsule"
52+
},
53+
{
54+
"id": "bd9a7518-66cb-4d50-9992-df3271aeb807",
55+
"position": {
56+
"x": 603.9999999999999,
57+
"y": -144.66666666666666
58+
},
59+
"selected": false,
60+
"type": "dataset"
4661
}
4762
],
48-
"timestamp": 1769626304514,
63+
"timestamp": 1769627284612,
4964
"viewport": {
50-
"x": 6,
51-
"y": 87,
65+
"x": -104,
66+
"y": 248,
5267
"zoom": 0.75
5368
}
5469
}

‎pipeline/main.nf‎

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
#!/usr/bin/env nextflow
2-
// hash:sha256:9b16fd2671702fcc56078aa8b25ef1fb8c069f03988557476eb9af8fad550618
2+
// hash:sha256:fd6acbeeb5285b14a52855521f09dd66b08f397d1e42c2bd7b7c2835107c03aa
33

44
// capsule - MOSuite-create
55
process capsule_mosuite_create_2 {
66
tag 'capsule-6541445'
7-
container "$REGISTRY_HOST/published/5ce5f88d-980d-4e61-b3a4-ef4a0ce48030:v3"
7+
container "$REGISTRY_HOST/published/5ce5f88d-980d-4e61-b3a4-ef4a0ce48030:v4"
88

99
cpus 1
1010
memory '7.5 GB'
@@ -26,11 +26,13 @@ process capsule_mosuite_create_2 {
2626
mkdir -p capsule/results && ln -s \$PWD/capsule/results /results
2727
mkdir -p capsule/scratch && ln -s \$PWD/capsule/scratch /scratch
2828
29+
ln -s "/tmp/data/nidap-1.0" "capsule/data/nidap-1.0" # id: bd9a7518-66cb-4d50-9992-df3271aeb807
30+
2931
echo "[${task.tag}] cloning git repo..."
3032
if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
31-
git clone --filter=tree:0 --branch v3.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
33+
git clone --filter=tree:0 --branch v4.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
3234
else
33-
git clone --branch v3.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
35+
git clone --branch v4.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
3436
fi
3537
mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
3638
rm -rf capsule-repo
@@ -50,7 +52,7 @@ process capsule_mosuite_clean_1 {
5052
container "$REGISTRY_HOST/published/ab07963e-d9e0-489e-b776-70f6ef2ef73b:v2"
5153

5254
cpus 1
53-
memory '7.5 GB'
55+
memory '3.75 GB'
5456

5557
publishDir "$RESULTS_PATH", saveAs: { filename -> new File(filename).getName() }
5658

@@ -67,7 +69,7 @@ process capsule_mosuite_clean_1 {
6769
6870
export CO_CAPSULE_ID=ab07963e-d9e0-489e-b776-70f6ef2ef73b
6971
export CO_CPUS=1
70-
export CO_MEMORY=8053063680
72+
export CO_MEMORY=4026531840
7173
7274
mkdir -p capsule
7375
mkdir -p capsule/data && ln -s \$PWD/capsule/data /data

0 commit comments

Comments
 (0)