Merge pull request #69 from seqeralabs/fix_cli_args_parsing

Fix parsing of extra args to tw CLI

Author: drpatelh

CHANGELOG.md

@@ -3,22 +3,27 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[0.5.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.5.0)] - 2024-10-24
+## [[0.5.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.5.0)] - 2024-11-12
 
 ### Credits
 
 Special thanks to the following for their contributions to the release:
 
 - [Adam Talbot](https://github.com/adamrtalbot)
+- [Esha Joshi](https://github.com/ejseqera)
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Maxime Garcia](https://github.com/maxulysse)
 - [Rob Syme](https://github.com/robsyme)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 
-[PR #61](https://github.com/seqeralabs/nf-aggregate/pull/61) - Remove dependency on external library/grape
-[PR #63](https://github.com/seqeralabs/nf-aggregate/pull/63) - Add `maxForks` setting for Seqera CLI to overcome API issues
-[PR #65](https://github.com/seqeralabs/nf-aggregate/pull/65) - Replace eclint GHA by pre-commit
+- [PR #61](https://github.com/seqeralabs/nf-aggregate/pull/61) - Remove dependency on external library/grape
+- [PR #63](https://github.com/seqeralabs/nf-aggregate/pull/63) - Add `maxForks` setting for Seqera CLI to overcome API issues
+- [PR #65](https://github.com/seqeralabs/nf-aggregate/pull/65) - Replace eclint GHA by pre-commit
+- [PR #67](https://github.com/seqeralabs/nf-aggregate/pull/67) - Update tests to use a non-fusion run from Seqera Cloud community/showcase
+- [PR #69](https://github.com/seqeralabs/nf-aggregate/pull/69) - Fix parsing of extra args to tw CLI
 
 ## [[0.4.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.4.0)] - 2024-07-26
 
@@ -32,9 +37,9 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Enhancements & fixes
 
-[PR #52](https://github.com/seqeralabs/nf-aggregate/pull/52) - Organise results folder structure by pipeline
-[PR #53](https://github.com/seqeralabs/nf-aggregate/pull/53) - Throw exception and terminate workflow in case config can't be read
-[PR #57](https://github.com/seqeralabs/nf-aggregate/pull/57) - Check if fusion is enabled via the Platform API
+- [PR #52](https://github.com/seqeralabs/nf-aggregate/pull/52) - Organise results folder structure by pipeline
+- [PR #53](https://github.com/seqeralabs/nf-aggregate/pull/53) - Throw exception and terminate workflow in case config can't be read
+- [PR #57](https://github.com/seqeralabs/nf-aggregate/pull/57) - Check if fusion is enabled via the Platform API
 
 ## [[0.3.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.3.0)] - 2024-07-01
 

modules/local/seqera_runs_dump/nextflow.config

@@ -1,7 +1,7 @@
 process {
     withName: 'SEQERA_RUNS_DUMP' {
         maxForks = 5
-        ext.args = { params.seqera_cli_extra_args ? params.seqera_cli_extra_args.split("\\s(?=--)") : '' }
+        ext.args = { params.seqera_cli_extra_args ? params.seqera_cli_extra_args.split(/[\s,]+(?=--)/).join(' ') : '' }
         ext.args2 = { params.skip_run_gantt ? '' : '--add-task-logs' }
         containerOptions = { params.java_truststore_path ? "--volume ${params.java_truststore_path}:${params.java_truststore_path}" : '' }
         publishDir = [

modules/local/seqera_runs_dump/tests/main.nf.test.snap

@@ -2,7 +2,7 @@
     "Should run without failures": {
         "content": [
             [
-                "service-info.json:md5,6988ae3ef3c822007075726ecc73ba9c",
+                "service-info.json:md5,75a5b8cded8f0ce9aab2125c0ee89f63",
                 "workflow-load.json:md5,4f02d5a24ab89aa648cd4346785c8f2c",
                 "workflow-metadata.json:md5,b37b4faeddf283a2c44cbe4000e4ab6e",
                 "workflow-metrics.json:md5,13a5b5d7447fad4a8baa053d1abf85e5",
@@ -12,9 +12,9 @@
             null
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-07-25T10:21:06.447483"
+        "timestamp": "2024-11-11T11:53:03.835699"
     }
-}
+}

subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap

@@ -2,10 +2,6 @@
     "Should run without failures": {
         "content": [
             [
-                {
-                    "id": "1oXDHFHywk3wR2",
-                    "workspace": "scidev/testing"
-                },
                 {
                     "id": "2lXd1j7OwZVfxh",
                     "workspace": "community/showcase"
@@ -14,6 +10,10 @@
                     "id": "38QXz4OfQDpwOV",
                     "workspace": "community/showcase"
                 },
+                {
+                    "id": "3iFMo0NtH1Byvy",
+                    "workspace": "community/showcase"
+                },
                 {
                     "id": "4Bi5xBK6E2Nbhj",
                     "workspace": "community/showcase"
@@ -25,9 +25,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-05-07T10:41:28.603749237"
+        "timestamp": "2024-11-11T11:32:52.476285"
     }
 }