diff --git a/package-lock.json b/package-lock.json
index 959594d72bbe696d513fc5ca572cbbeb137fa20c..be37a3e534aed19236f7bfe8186a5a27bf938ed0 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -6640,9 +6640,9 @@
}
},
"node_modules/vite": {
- "version": "5.2.12",
- "resolved": "https://registry.npmjs.org/vite/-/vite-5.2.12.tgz",
- "integrity": "sha512-/gC8GxzxMK5ntBwb48pR32GGhENnjtY30G4A0jemunsBkiEZFw60s8InGpN8gkhHEkjnRK1aSAxeQgwvFhUHAA==",
+ "version": "5.2.13",
+ "resolved": "https://registry.npmjs.org/vite/-/vite-5.2.13.tgz",
+ "integrity": "sha512-SSq1noJfY9pR3I1TUENL3rQYDQCFqgD+lM6fTRAM8Nv6Lsg5hDLaXkjETVeBt+7vZBCMoibD+6IWnT2mJ+Zb/A==",
"dev": true,
"dependencies": {
"esbuild": "^0.20.1",
diff --git a/src/components/workflows/modals/ArbitraryWorkflowModal.vue b/src/components/workflows/modals/ArbitraryWorkflowModal.vue
index 8a9a45d3a3f25d3d6e1e41308b9b10718b7231b6..132dd4a27f224721d79fb8aeaa6d96e7b0a60029 100644
--- a/src/components/workflows/modals/ArbitraryWorkflowModal.vue
+++ b/src/components/workflows/modals/ArbitraryWorkflowModal.vue
@@ -66,7 +66,7 @@ const executionEnvironmentState = reactive<{
cluster: boolean;
}>({
cli: false,
- cluster: true,
+ cluster: false,
});
const formState = reactive<{
@@ -155,23 +155,33 @@ const resourcePathPrefix = computed<string>(() => {
return resourcePath.slice(0, ind - 1);
});
-const nextflowConfig = computed<string>(
- () => `aws {
- client {
- endpoint = '${environment.S3_URL}'
- s3PathStyleAccess = true
- }
+const nextflowConfig = computed<string>(() => {
+ if (executionEnvironmentState.cluster) {
+ return `// Nextflow config to emulate CloWM native execution
+aws {
accessKey = '${s3KeyStore.keys[0]?.access_key ?? ""}'
secretKey = '${s3KeyStore.keys[0]?.secret_key ?? ""}'
+ client {
+ endpoint = '${environment.S3_URL}'
+ s3PathStyleAccess = true
+ }
}
+// Docker container options
docker {
enabled = true
- runOptions = "-u \\$(id -u):\\$(id -g) -q -v ${executionEnvironmentState.cluster ? `${resourcePathPrefix.value}:${resourcePathPrefix.value}:ro` : ""}"
+ runOptions = "-u \\$(id -u):\\$(id -g) -q \\
+ -v ${resourcePathPrefix.value}:${resourcePathPrefix.value}:ro \\
+ -v /var/lib/lxcfs/proc/cpuinfo:/proc/cpuinfo:rw \\
+ -v /var/lib/lxcfs/proc/diskstats:/proc/diskstats:rw \\
+ -v /var/lib/lxcfs/proc/meminfo:/proc/meminfo:rw \\
+ -v /var/lib/lxcfs/proc/stat:/proc/stat:rw \\
+ -v /var/lib/lxcfs/proc/swaps:/proc/swaps:rw \\
+ -v /var/lib/lxcfs/proc/uptime:/proc/uptime:rw"
}
// Disable unwanted features
-tower.enabled = false
+// Attention: Docker is the only supported container engine so far!
weblog.enabled = false
shifter.enabled = false
singularity.enabled = false
@@ -180,18 +190,134 @@ charliecloud.enabled = false
dag.enabled = false
trace.enabled = false
+// Nextflow provenance tracking plugin
+plugins {
+ id 'nf-prov'
+}
+
+prov {
+ enabled = true
+ formats {
+ legacy {
+ file = "./nf-prov_manifest.json"
+ overwrite = true
+ }
+ bco {
+ file = "./nf-prov_bco.json"
+ overwrite = true
+ }
+ dag {
+ file = "./nf-prov_dag.html"
+ overwrite = true
+ }
+ }
+}
+
executor {
submitRateLimit = '5 sec'
}
+// Process resource labels currently used by CloWM
+process {
+ executor = 'slurm'
+ container = 'ubuntu:22.04'
+ cpus = { 2 }
+ memory = { 4000.MB }
+ maxErrors = '-1'
+
+ // Process-specific resource requirements
+ withLabel:process_single {
+ cpus = { 1 }
+ memory = { 6000.MB }
+ }
+ withLabel:process_low {
+ cpus = { 2 }
+ memory = { 12000.MB }
+ }
+ withLabel:process_medium {
+ cpus = { 6 }
+ memory = { 36000.MB }
+ }
+ withLabel:process_high {
+ cpus = { 12 }
+ memory = { 72000.MB }
+ }
+ withLabel:process_high_memory {
+ memory = { 200000.MB }
+ }
+ withLabel:error_ignore {
+ errorStrategy = 'ignore'
+ }
+ withLabel: highmemXLarge {
+ cpus = { 28 }
+ memory = {470000.MB}
+ }
+ withLabel: computeXLarge {
+ cpus = {28}
+ memory = {470000.MB}
+ }
+ withLabel: highmemLarge {
+ cpus = {28}
+ memory = {240000.MB}
+ }
+ withLabel: highmemMedium {
+ cpus = {14}
+ memory = {120000.MB}
+ }
+ withLabel: large {
+ cpus = {28}
+ memory = {64000.MB}
+ }
+ withLabel: medium {
+ cpus = {14}
+ memory = {32000.MB}
+ }
+ withLabel: small {
+ cpus = {8}
+ memory = {16000.MB}
+ }
+ withLabel: mini {
+ cpus = {4}
+ memory = {8000.MB}
+ }
+ withLabel: tiny {
+ cpus = {1}
+ memory = {2000.MB}
+ }
+}`;
+ }
+ return `aws {
+ client {
+ endpoint = '${environment.S3_URL}'
+ s3PathStyleAccess = true
+ }
+ accessKey = '${s3KeyStore.keys[0]?.access_key ?? ""}'
+ secretKey = '${s3KeyStore.keys[0]?.secret_key ?? ""}'
+}
+
+docker {
+ enabled = true
+ runOptions = "-u \\$(id -u):\\$(id -g) -q"
+}
+
+// Disable unwanted features
+tower.enabled = false
+weblog.enabled = false
+shifter.enabled = false
+singularity.enabled = false
+podman.enabled = false
+charliecloud.enabled = false
+dag.enabled = true
+trace.enabled = true
+
process {
- executor = '${executionEnvironmentState.cluster ? "slurm" : "local"}'
+ executor = 'local'
container = 'ubuntu:22.04'
cpus = { 2 }
memory = { 4000.MB }
}
-`,
-);
+`;
+});
const configDownloadUrl = computed<string>(() =>
createDownloadUrl(nextflowConfig.value, "text/plain"),
@@ -268,12 +394,13 @@ onMounted(() => {
<bootstrap-modal
:modalId="modalId"
:static-backdrop="false"
- modal-label="Create Workflow Modal"
+ modal-label="Test My Workflow Modal"
v-on="{ 'hidden.bs.modal': modalClosed }"
size-modifier-modal="lg"
>
- <template v-slot:header>Start arbitrary Workflow</template>
+ <template v-slot:header>Test workflow prior registration</template>
<template v-slot:body>
+ <h5>Choose your execution environment</h5>
<div class="btn-group justify-content-center w-100 mb-2" role="group">
<input
type="radio"
@@ -286,7 +413,7 @@ onMounted(() => {
:value="false"
/>
<label class="btn btn-outline-primary" for="clowm-outlined"
- >CloWM Execution</label
+ >CloWM native execution</label
>
<input
@@ -315,7 +442,7 @@ onMounted(() => {
:value="false"
/>
<label class="btn btn-outline-primary" for="laptop-outlined"
- >Own computer</label
+ >Personal computer</label
>
<input
@@ -328,19 +455,26 @@ onMounted(() => {
:value="true"
/>
<label class="btn btn-outline-primary" for="cluster-outlined"
- >Dev Cluster</label
+ >Emulated CloWM environment</label
>
</div>
- <h6>Nextflow config</h6>
- <pre class="w-100 rounded-1"><code>{{ nextflowConfig }}</code></pre>
- <h6>Start your workflow</h6>
- <p>
- Download the config file, run your nextflow workflow and point to the
- downloaded config file
+ <p v-if="executionEnvironmentState.cluster">
+ To emulate the CloWM native execution environment (e.g. docker
+ configuration, S3 access, resource labels etc.) on the workflow
+ development system, please download and use the Nextflow configuration
+ file (<code>clowm-nextflow.config</code>) as described below.
+ </p>
+ <p v-else>
+ To emulate a basic CloWM native execution environment (e.g. docker
+ configuration, S3 access etc.) on your personal computer, please
+ download and use the Nextflow configuration file
+ (<code>clowm-nextflow.config</code>) as described below.
</p>
<pre
class="rounded-1 w-100"
><code>nextflow run /path/to/main.nf -c clowm-nextflow.config ...</code></pre>
+ <h6>clowm-nextflow.config:</h6>
+ <pre class="w-100 rounded-1"><code>{{ nextflowConfig }}</code></pre>
</div>
<form
v-else
diff --git a/src/views/workflows/ListWorkflowsView.vue b/src/views/workflows/ListWorkflowsView.vue
index d6167b396b94758200311c9e65cca1191ae0a9fc..9ee51bded4b9037152defb23bd4f65611b73fe54 100644
--- a/src/views/workflows/ListWorkflowsView.vue
+++ b/src/views/workflows/ListWorkflowsView.vue
@@ -39,7 +39,9 @@ const filterFunctionMapping: Record<
function filterWorkflowByString(workflow: WorkflowOut): boolean {
return workflowsState.filterString.length > 0
- ? workflow.name.includes(workflowsState.filterString)
+ ? workflow.name
+ .toLowerCase()
+ .includes(workflowsState.filterString.toLowerCase())
: true;
}