1.3.4 patch release

CHANGELOG.md

@@ -3,6 +3,11 @@
 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).
 
+## [1.3.4] - 2026-03-09
+
+- Added `software_versions.yml` to the `iridanext.output.json.gz` file to track module container updates. [PR #33](https://github.com/phac-nml/fetchdatairidanext/pull/33)
+- Move `CUSTOM_SRATOOLSNCBISETTINGS` to a local module, remove from nf-core, and update `sra-toolkit` to `3.2.1`. [PR #33](https://github.com/phac-nml/fetchdatairidanext/pull/33)
+
 ## [1.3.3] - 2026-03-06
 
 ### `Changed`
@@ -80,6 +85,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Initial release of fetchdatairidanext pipeline which will download reads from NCBI/INSDC archives.
 
+[1.3.4]: https://github.com/phac-nml/fetchdatairidanext/releases/tag/1.3.4
 [1.3.3]: https://github.com/phac-nml/fetchdatairidanext/releases/tag/1.3.3
 [1.3.2]: https://github.com/phac-nml/fetchdatairidanext/releases/tag/1.3.2
 [1.3.1]: https://github.com/phac-nml/fetchdatairidanext/releases/tag/1.3.1

conf/iridanext.config

@@ -6,7 +6,10 @@ iridanext {
         validate = true
         files {
             idkey = "irida_id"
-            global = ["**/prefetch/failures_report.csv"]
+            global = [
+                "**/prefetch/failures_report.csv",
+                "**/pipeline_info/software_versions.yml"
+                ]
             samples = ["**/reads/*.fastq.gz"]
         }
     }

modules.json

@@ -9,11 +9,6 @@
                         "branch": "master",
                         "git_sha": "1526dc37227a1101bdca25339337362e187a6b3b",
                         "installed_by": ["modules"]
-                    },
-                    "custom/sratoolsncbisettings": {
-                        "branch": "master",
-                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
-                        "installed_by": ["modules"]
                     }
                 }
             }

modules/nf-core/custom/sratoolsncbisettings/main.nf → modules/local/sratoolsncbisettings/main.nf

@@ -4,8 +4,8 @@ process CUSTOM_SRATOOLSNCBISETTINGS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:3.0.8--h9f5acd7_0' :
-        'biocontainers/sra-tools:3.0.8--h9f5acd7_0' }"
+        'https://depot.galaxyproject.org/singularity/sra-tools:3.2.1--h4304569_1' :
+        'biocontainers/sra-tools:3.2.1--h4304569_1' }"
 
     output:
     path('*.mkfg')     , emit: ncbi_settings

modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config → modules/local/sratoolsncbisettings/tests/nextflow.config

@@ -13,4 +13,4 @@ process {
             "-v ${params.settings_path}:${params.settings_path}"
         }
     }
-}
+}

nextflow.config

@@ -205,7 +205,7 @@ manifest {
     description     = """IRIDA Next pipeline for fetching data from INSDC Databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.3.3'
+    version         = '1.3.4'
     doi             = ''
     defaultBranch   = 'main'
 }

subworkflows/local/fastq_download_prefetch_fasterqdump_sratools/main.nf

@@ -1,5 +1,5 @@
-include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/nf-core/custom/sratoolsncbisettings/main'
-include { SRATOOLS_PREFETCH           } from '../../../modules/local/prefetch/main'
+include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/local/sratoolsncbisettings/main'
+include { SRATOOLS_PREFETCH           } from '../../../modules/local/sratools/prefetch/main'
 include { PREFETCH_CHECKER            } from '../../../modules/local/prefetchchecker/main'
 include { SRATOOLS_FASTERQDUMP        } from '../../../modules/local/sratools/fasterqdump/main'
 

tests/data/prefetch_errors_iridanext.output.json

@@ -1,6 +1,9 @@
 {
     "files": {
         "global": [
+            {
+                "path": "pipeline_info/software_versions.yml"
+            },
             {
                 "path": "prefetch/failures_report.csv"
             }

tests/data/test_fetch_iridanext.output.json

@@ -1,6 +1,9 @@
 {
     "files": {
         "global": [
+            {
+                "path": "pipeline_info/software_versions.yml"
+            },
             {
                 "path": "prefetch/failures_report.csv"
             }

tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap

@@ -23,7 +23,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
+                    "versions.yml:md5,583cd2949d8d481fead1dd0124a35dc5",
                     "versions.yml:md5,67c595bdcd89abea73efccf7ce9adc4e",
                     "versions.yml:md5,c585a49fc382d71066a4c55fe7409aef"
                 ],
@@ -48,7 +48,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
+                    "versions.yml:md5,583cd2949d8d481fead1dd0124a35dc5",
                     "versions.yml:md5,67c595bdcd89abea73efccf7ce9adc4e",
                     "versions.yml:md5,c585a49fc382d71066a4c55fe7409aef"
                 ]
@@ -58,6 +58,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2026-03-06T09:17:36.4522704"
+        "timestamp": "2026-03-09T10:14:58.957319301"
     }
 }