Edited app-panel.json, nextflow.json, pipeline-layout.json, main.nf; and changes in 1 other files

Author: kelly-sovacool

.codeocean/app-panel.json

@@ -1,6 +1,7 @@
 {
 	"version": 1,
 	"processes": [
-		"capsule_mosuite_create_2"
+		"capsule_mosuite_create_2",
+		"capsule_mosuite_clean_1"
 	]
 }

.codeocean/datasets.json

@@ -0,0 +1,9 @@
+{
+	"version": 1,
+	"attached_datasets": [
+		{
+			"id": "4ea90259-b1ac-491b-8571-5c25a8a98529",
+			"mount": "moo-create"
+		}
+	]
+}

.codeocean/nextflow.json

@@ -7,7 +7,7 @@
 				"id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b",
 				"name": "MOSuite-clean",
 				"slug": "5801113",
-				"version": 1,
+				"version": 2,
 				"app_panel": true
 			},
 			"resources": {
@@ -16,20 +16,23 @@
 			},
 			"inputs": [
 				{
-					"id": "uqbFE30XQBTDxBxR",
+					"id": "NLgJ8e32jH3YibWL",
 					"source_id": "capsule_mosuite_create_2",
 					"type": "capsule",
 					"name": "MOSuite-create"
 				}
-			]
+			],
+			"results": {
+				"id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b"
+			}
 		},
 		{
 			"name": "capsule_mosuite_create_2",
 			"capsule": {
 				"id": "5ce5f88d-980d-4e61-b3a4-ef4a0ce48030",
 				"name": "MOSuite-create",
 				"slug": "6541445",
-				"version": 2,
+				"version": 3,
 				"app_panel": true
 			},
 			"resources": {

.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": [
@@ -16,7 +21,7 @@
 				"x": 842.6666666666667,
 				"y": 270
 			},
-			"selected": false,
+			"selected": true,
 			"type": "capsule"
 		},
 		{
@@ -36,11 +41,11 @@
 				"x": 718.6666666666666,
 				"y": 31.333333333333343
 			},
-			"selected": true,
+			"selected": false,
 			"type": "capsule"
 		}
 	],
-	"timestamp": 1769554760195,
+	"timestamp": 1769626304514,
 	"viewport": {
 		"x": 6,
 		"y": 87,

pipeline/main.nf

@@ -1,10 +1,10 @@
 #!/usr/bin/env nextflow
-// hash:sha256:e60c74eb0db9870da170bd3833dbe435cba6b383333fc48223204b0a17b1e6f0
+// hash:sha256:9b16fd2671702fcc56078aa8b25ef1fb8c069f03988557476eb9af8fad550618
 
 // capsule - MOSuite-create
 process capsule_mosuite_create_2 {
 	tag 'capsule-6541445'
-	container "$REGISTRY_HOST/published/5ce5f88d-980d-4e61-b3a4-ef4a0ce48030:v2"
+	container "$REGISTRY_HOST/published/5ce5f88d-980d-4e61-b3a4-ef4a0ce48030:v3"
 
 	cpus 1
 	memory '7.5 GB'
@@ -28,9 +28,9 @@ process capsule_mosuite_create_2 {
 
 	echo "[${task.tag}] cloning git repo..."
 	if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
-		git clone --filter=tree:0 --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
+		git clone --filter=tree:0 --branch v3.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
 	else
-		git clone --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
+		git clone --branch v3.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
 	fi
 	mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
 	rm -rf capsule-repo
@@ -47,14 +47,19 @@ process capsule_mosuite_create_2 {
 // capsule - MOSuite-clean
 process capsule_mosuite_clean_1 {
 	tag 'capsule-5801113'
-	container "$REGISTRY_HOST/published/ab07963e-d9e0-489e-b776-70f6ef2ef73b:v1"
+	container "$REGISTRY_HOST/published/ab07963e-d9e0-489e-b776-70f6ef2ef73b:v2"
 
 	cpus 1
 	memory '7.5 GB'
 
+	publishDir "$RESULTS_PATH", saveAs: { filename -> new File(filename).getName() }
+
 	input:
 	path 'capsule/data/'
 
+	output:
+	path 'capsule/results/*'
+
 	script:
 	"""
 	#!/usr/bin/env bash
@@ -71,9 +76,9 @@ process capsule_mosuite_clean_1 {
 
 	echo "[${task.tag}] cloning git repo..."
 	if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
-		git clone --filter=tree:0 --branch v1.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-5801113.git" capsule-repo
+		git clone --filter=tree:0 --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-5801113.git" capsule-repo
 	else
-		git clone --branch v1.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-5801113.git" capsule-repo
+		git clone --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-5801113.git" capsule-repo
 	fi
 	mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
 	rm -rf capsule-repo