fix: bump capsule versions

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/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": {
@@ -29,7 +29,7 @@
 				"id": "5ce5f88d-980d-4e61-b3a4-ef4a0ce48030",
 				"name": "MOSuite-create",
 				"slug": "6541445",
-				"version": 2,
+				"version": 3,
 				"app_panel": true
 			},
 			"resources": {

pipeline/main.nf

@@ -1,10 +1,10 @@
 #!/usr/bin/env nextflow
-// hash:sha256:e60c74eb0db9870da170bd3833dbe435cba6b383333fc48223204b0a17b1e6f0
+// hash:sha256:4b0bcda131abb27fe9f74befd9dd96e7bdb41c86bd4eef2bba0c0bccf8715402
 
 // 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 "[${task.tag}] cloning git repo..."
 	if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
-		git clone --filter=tree:0 --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
+		git clone --filter=tree:0 --branch v3.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
 	else
-		git clone --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
+		git clone --branch v3.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
 	fi
 	mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
 	rm -rf capsule-repo
@@ -47,7 +47,7 @@ process capsule_mosuite_create_2 {
 // capsule - MOSuite-clean
 process capsule_mosuite_clean_1 {
 	tag 'capsule-5801113'
-	container "$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'
@@ -71,9 +71,9 @@ 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