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Fix nextflow issues #663

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merged 4 commits into from
Mar 19, 2024
Merged

Fix nextflow issues #663

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d26ccc9
simplify test
rcannood Mar 15, 2024
af5d322
simplify stubrun id check
rcannood Mar 15, 2024
57d456c
change search key
rcannood Mar 15, 2024
f0ede1a
fix test
rcannood Mar 19, 2024
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4 changes: 2 additions & 2 deletions src/main/resources/io/viash/platforms/nextflow/channel/channelFromParams.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -60,9 +60,9 @@ private List<Tuple2<String, Map<String, Object>>> _paramsToParamSets(Map params,
// Process ID
def id = tup[0] ?: globalID

if (workflow.stubRun) {
if (workflow.stubRun && !id) {
// if stub run, explicitly add an id if missing
id = id ? id : "stub${index}"
id = "stub${index}"
}
assert id != null: "Each parameter set should have at least an 'id'"

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11 changes: 9 additions & 2 deletions src/test/scala/io/viash/platforms/nextflow/NextflowScriptTest.scala
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Expand Up @@ -153,8 +153,15 @@ class NextflowScriptTest extends AnyFunSuite with BeforeAndAfterAll {
)

assert(exitCode == 0, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
assert(stdOut.contains("base:step1_alias:proc"))
assert(stdOut.contains("base:step1:proc"))
// Note: Nextflow 23.04 changed the way processes are printed in the log
// original:
// [info] [30/b6eaaf] process > alias:base:step1:processWf:... [100%] 1 of 1 ✔
// [info] [bf/166913] process > alias:base:step1_alias:proc... [100%] 1 of 1 ✔
// since nextflow 23.04:
// [info] [31/1c0834] ali…cessWf:step1_process (one) | 1 of 1 ✔
// [info] [f1/e92549] ali…:step1_alias_process (one) | 1 of 1 ✔
assert(stdOut.contains(":step1_alias:proc") || stdOut.contains(":step1_alias_process"))
assert(stdOut.contains(":step1:proc") || stdOut.contains(":step1_process"))
assert(!stdOut.contains("Key for module 'step1' is duplicated"))
}

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