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Fix: Organise results folder structure by pipeline #52

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merged 3 commits into from
Jul 25, 2024
Merged

Fix: Organise results folder structure by pipeline #52

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c9aec68
Merge pull request #51 from seqeralabs/dev
drpatelh Jul 1, 2024
9c7c936
keep scope of linked map local
FriederikeHanssen Jul 24, 2024
581f97a
update snapshot
FriederikeHanssen Jul 25, 2024
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4 changes: 2 additions & 2 deletions modules/local/seqera_runs_dump/functions.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -47,8 +47,8 @@ Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword)
if (workspaceId) {
def workflowResponse = client.get(path: "/workflow/${runId}", query: ["workspaceId":workspaceId], headers: authHeader)
if (workflowResponse.statusCode == 200) {
metaMap = workflowResponse?.json?.workflow?.subMap("runName", "workDir", "projectName")
config = new ConfigSlurper().parse( workflowResponse?.json?.workflow?.configText )
def metaMap = workflowResponse?.json?.workflow?.subMap("runName", "workDir", "projectName")
def config = new ConfigSlurper().parse( workflowResponse?.json?.workflow?.configText )
metaMap.fusion = config.fusion.enabled

return metaMap ?: [:]
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6 changes: 3 additions & 3 deletions modules/local/seqera_runs_dump/tests/main.nf.test.snap
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Expand Up @@ -2,7 +2,7 @@
"Should run without failures": {
"content": [
[
"service-info.json:md5,108f149aafa287bb56d715c0c7ee0359",
"service-info.json:md5,72586e82ad2064d1a90008c7956d80d8",
"workflow-load.json:md5,4f02d5a24ab89aa648cd4346785c8f2c",
"workflow-metadata.json:md5,b37b4faeddf283a2c44cbe4000e4ab6e",
"workflow-metrics.json:md5,13a5b5d7447fad4a8baa053d1abf85e5",
Expand All @@ -13,8 +13,8 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-05-20T15:32:40.565622058"
"timestamp": "2024-07-25T10:21:06.447483"
}
}
3 changes: 2 additions & 1 deletion workflows/nf_aggregate/main.nf
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Expand Up @@ -21,7 +21,7 @@ workflow NF_AGGREGATE {
skip_multiqc // val: Skip MultiQC
java_truststore_path // val: Path to java truststore if using private certs
java_truststore_password // val: Password for java truststore if using private certs

main:

ch_versions = Channel.empty()
Expand All @@ -30,6 +30,7 @@ workflow NF_AGGREGATE {
//
// MODULE: Fetch run information via the Seqera CLI
//

SEQERA_RUNS_DUMP (
ids,
seqera_api_endpoint,
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