diff --git a/CHANGELOG.md b/CHANGELOG.md index 8f693a6..8ef0512 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/conf/iridanext.config b/conf/iridanext.config index 739532c..f00ef77 100644 --- a/conf/iridanext.config +++ b/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"] } } diff --git a/modules.json b/modules.json index 9a4678a..3a890bb 100644 --- a/modules.json +++ b/modules.json @@ -9,11 +9,6 @@ "branch": "master", "git_sha": "1526dc37227a1101bdca25339337362e187a6b3b", "installed_by": ["modules"] - }, - "custom/sratoolsncbisettings": { - "branch": "master", - "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620", - "installed_by": ["modules"] } } } diff --git a/modules/local/prefetch/environment.yml b/modules/local/sratools/prefetch/environment.yml similarity index 100% rename from modules/local/prefetch/environment.yml rename to modules/local/sratools/prefetch/environment.yml diff --git a/modules/local/prefetch/main.nf b/modules/local/sratools/prefetch/main.nf similarity index 100% rename from modules/local/prefetch/main.nf rename to modules/local/sratools/prefetch/main.nf diff --git a/modules/local/prefetch/templates/retry_with_backoff.sh b/modules/local/sratools/prefetch/templates/retry_with_backoff.sh similarity index 100% rename from modules/local/prefetch/templates/retry_with_backoff.sh rename to modules/local/sratools/prefetch/templates/retry_with_backoff.sh diff --git a/modules/nf-core/custom/sratoolsncbisettings/environment.yml b/modules/local/sratoolsncbisettings/environment.yml similarity index 100% rename from modules/nf-core/custom/sratoolsncbisettings/environment.yml rename to modules/local/sratoolsncbisettings/environment.yml diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/local/sratoolsncbisettings/main.nf similarity index 89% rename from modules/nf-core/custom/sratoolsncbisettings/main.nf rename to modules/local/sratoolsncbisettings/main.nf index ba9441c..f20a590 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/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 diff --git a/modules/nf-core/custom/sratoolsncbisettings/meta.yml b/modules/local/sratoolsncbisettings/meta.yml similarity index 100% rename from modules/nf-core/custom/sratoolsncbisettings/meta.yml rename to modules/local/sratoolsncbisettings/meta.yml diff --git a/modules/nf-core/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh b/modules/local/sratoolsncbisettings/templates/detect_ncbi_settings.sh similarity index 100% rename from modules/nf-core/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh rename to modules/local/sratoolsncbisettings/templates/detect_ncbi_settings.sh diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/local/sratoolsncbisettings/tests/main.nf.test similarity index 100% rename from modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test rename to modules/local/sratoolsncbisettings/tests/main.nf.test diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/local/sratoolsncbisettings/tests/main.nf.test.snap similarity index 100% rename from modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap rename to modules/local/sratoolsncbisettings/tests/main.nf.test.snap diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/local/sratoolsncbisettings/tests/nextflow.config similarity index 99% rename from modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config rename to modules/local/sratoolsncbisettings/tests/nextflow.config index c4a96e9..f24f8c5 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config +++ b/modules/local/sratoolsncbisettings/tests/nextflow.config @@ -13,4 +13,4 @@ process { "-v ${params.settings_path}:${params.settings_path}" } } -} \ No newline at end of file +} diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml b/modules/local/sratoolsncbisettings/tests/tags.yml similarity index 100% rename from modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml rename to modules/local/sratoolsncbisettings/tests/tags.yml diff --git a/nextflow.config b/nextflow.config index f586d2f..01c574e 100644 --- a/nextflow.config +++ b/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' } diff --git a/subworkflows/local/fastq_download_prefetch_fasterqdump_sratools/main.nf b/subworkflows/local/fastq_download_prefetch_fasterqdump_sratools/main.nf index ebf1400..2fbbec5 100644 --- a/subworkflows/local/fastq_download_prefetch_fasterqdump_sratools/main.nf +++ b/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' diff --git a/tests/data/prefetch_errors_iridanext.output.json b/tests/data/prefetch_errors_iridanext.output.json index df07228..e40dcdf 100644 --- a/tests/data/prefetch_errors_iridanext.output.json +++ b/tests/data/prefetch_errors_iridanext.output.json @@ -1,6 +1,9 @@ { "files": { "global": [ + { + "path": "pipeline_info/software_versions.yml" + }, { "path": "prefetch/failures_report.csv" } diff --git a/tests/data/test_fetch_iridanext.output.json b/tests/data/test_fetch_iridanext.output.json index d8ecedf..9625103 100644 --- a/tests/data/test_fetch_iridanext.output.json +++ b/tests/data/test_fetch_iridanext.output.json @@ -1,6 +1,9 @@ { "files": { "global": [ + { + "path": "pipeline_info/software_versions.yml" + }, { "path": "prefetch/failures_report.csv" } diff --git a/tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap b/tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap index 878b9a1..2fb0750 100644 --- a/tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap +++ b/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" } } \ No newline at end of file