feat: attach default dataset; fix CO link

Author: kelly-sovacool

.codeocean/app-panel.json

@@ -1,5 +1,15 @@
 {
 	"version": 1,
+	"general": {
+		"title": "MOSuite-pipeline",
+		"instructions": "differential multi-omics analysis pipeline"
+	},
+	"datasets": [
+		{
+			"id": "bd9a7518-66cb-4d50-9992-df3271aeb807",
+			"name": "bulk RNA-seq training dataset"
+		}
+	],
 	"processes": [
 		"capsule_mosuite_create_2",
 		"capsule_mosuite_clean_1"

.codeocean/datasets.json

@@ -0,0 +1,9 @@
+{
+	"version": 1,
+	"attached_datasets": [
+		{
+			"id": "bd9a7518-66cb-4d50-9992-df3271aeb807",
+			"mount": "nidap-1.0"
+		}
+	]
+}

.codeocean/nextflow.json

@@ -12,7 +12,7 @@
 			},
 			"resources": {
 				"cpus": 1,
-				"memory": 8
+				"memory": 4
 			},
 			"inputs": [
 				{
@@ -21,7 +21,10 @@
 					"type": "capsule",
 					"name": "MOSuite-create"
 				}
-			]
+			],
+			"results": {
+				"id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b"
+			}
 		},
 		{
 			"name": "capsule_mosuite_create_2",
@@ -34,7 +37,7 @@
 			},
 			"resources": {
 				"cpus": 1,
-				"memory": 8
+				"memory": 4
 			}
 		}
 	]

.codeocean/pipeline-layout.json

@@ -4,6 +4,11 @@
 			"id": "xy-edge__capsule_mosuite_create_2-capsule_mosuite_clean_1",
 			"source": "capsule_mosuite_create_2",
 			"target": "capsule_mosuite_clean_1"
+		},
+		{
+			"id": "xy-edge__capsule_mosuite_clean_1-results",
+			"source": "capsule_mosuite_clean_1",
+			"target": "results"
 		}
 	],
 	"nodes": [
@@ -40,10 +45,10 @@
 			"type": "capsule"
 		}
 	],
-	"timestamp": 1769554760195,
+	"timestamp": 1769624886972,
 	"viewport": {
-		"x": 6,
-		"y": 87,
+		"x": -138,
+		"y": 162,
 		"zoom": 0.75
 	}
 }

README.md

@@ -1,3 +1,3 @@
 # MOSuite-CodeOcean pipeline
 
-- [Code Ocean pipeline](https://poc-nci.codeocean.io/capsule/1830412/tree)
+- [Code Ocean pipeline](https://poc-nci.codeocean.io/capsule/2912065/tree)

pipeline/main.nf

@@ -1,13 +1,13 @@
 #!/usr/bin/env nextflow
-// hash:sha256:4b0bcda131abb27fe9f74befd9dd96e7bdb41c86bd4eef2bba0c0bccf8715402
+// hash:sha256:fc7707155fa4333219b4c0480ac4dd17544f4f655aaee1688d233ee4abbbd98b
 
 // capsule - MOSuite-create
 process capsule_mosuite_create_2 {
 	tag 'capsule-6541445'
 	container "$REGISTRY_HOST/published/5ce5f88d-980d-4e61-b3a4-ef4a0ce48030:v3"
 
 	cpus 1
-	memory '7.5 GB'
+	memory '3.75 GB'
 
 	output:
 	path 'capsule/results/*', emit: to_capsule_mosuite_clean_1_1
@@ -19,7 +19,7 @@ process capsule_mosuite_create_2 {
 
 	export CO_CAPSULE_ID=5ce5f88d-980d-4e61-b3a4-ef4a0ce48030
 	export CO_CPUS=1
-	export CO_MEMORY=8053063680
+	export CO_MEMORY=4026531840
 
 	mkdir -p capsule
 	mkdir -p capsule/data && ln -s \$PWD/capsule/data /data
@@ -50,19 +50,24 @@ process capsule_mosuite_clean_1 {
 	container "$REGISTRY_HOST/published/ab07963e-d9e0-489e-b776-70f6ef2ef73b:v2"
 
 	cpus 1
-	memory '7.5 GB'
+	memory '3.75 GB'
+
+	publishDir "$RESULTS_PATH", saveAs: { filename -> new File(filename).getName() }
 
 	input:
 	path 'capsule/data/'
 
+	output:
+	path 'capsule/results/*'
+
 	script:
 	"""
 	#!/usr/bin/env bash
 	set -e
 
 	export CO_CAPSULE_ID=ab07963e-d9e0-489e-b776-70f6ef2ef73b
 	export CO_CPUS=1
-	export CO_MEMORY=8053063680
+	export CO_MEMORY=4026531840
 
 	mkdir -p capsule
 	mkdir -p capsule/data && ln -s \$PWD/capsule/data /data