From eccff3102b79dfbf4e498b202c2fd2a4db27d4ae Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 6 Nov 2024 15:39:47 +0000 Subject: [PATCH 01/17] post patch version bump --- .nf-core.yml | 2 +- CHANGELOG.md | 8 ++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 4 files changed, 12 insertions(+), 4 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 561994da..e679aab8 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -17,5 +17,5 @@ template: outdir: . skip_features: - igenomes - version: 1.5.2 + version: 1.5.3dev update: null diff --git a/CHANGELOG.md b/CHANGELOG.md index 47057a52..577d6437 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,14 @@ 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). +## dev - [unreleased] + +### `Added` + +### `Changed` + +### `Fixed` + ## 1.5.3 - 2024-11-06 ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index bf9df924..42478dee 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/demultiplex + This report has been generated by the nf-core/demultiplex analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-demultiplex-methods-description": diff --git a/nextflow.config b/nextflow.config index fa7fb516..5a2471ad 100755 --- a/nextflow.config +++ b/nextflow.config @@ -265,7 +265,7 @@ manifest { description = """Demultiplexing pipeline for Illumina sequencing data""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '1.5.3' + version = '1.5.3dev' doi = '10.5281/zenodo.7153103' } From e4f429e4a2bd2ca77fc523f987db2232a60a21ba Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 20 Nov 2024 22:05:40 +0000 Subject: [PATCH 02/17] test: fix workflow dispatch --- .github/workflows/awsfulltest.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 8e4df67f..57519ce9 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -19,9 +19,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: octokit/request-action@v2.x + if: github.event_name != 'workflow_dispatch' id: check_approvals with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - id: test_variables @@ -32,9 +33,6 @@ jobs: test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 - # TODO nf-core: You can customise AWS full pipeline tests as required - # Add full size test data (but still relatively small datasets for few samples) - # on the `test_full.config` test runs with only one set of parameters with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} From 3a69cc5b77101e0888b09b3f140eb8137790203a Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 20 Nov 2024 22:06:25 +0000 Subject: [PATCH 03/17] test: add lenient mode to fix parameter validation in test full --- CHANGELOG.md | 2 ++ nextflow.config | 1 + 2 files changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 577d6437..4b65bbc8 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#288](https://github.com/nf-core/demultiplex/pull/288) Fix `test_full` by validating parameters in `lenientMode` and fix workflow megatest workflow dispatch. + ## 1.5.3 - 2024-11-06 ### `Added` diff --git a/nextflow.config b/nextflow.config index 5a2471ad..47cc7705 100755 --- a/nextflow.config +++ b/nextflow.config @@ -276,6 +276,7 @@ plugins { validation { defaultIgnoreParams = ["genomes"] + lenientMode = true help { enabled = true command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " From 09877da0e0c66f20bbb403e04ccd01d8f4004614 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 21 Nov 2024 18:05:42 +0000 Subject: [PATCH 04/17] test: enforce meta.id always be a string after nf-schema lenientMode is true --- workflows/demultiplex.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf index cc22534d..9597883e 100644 --- a/workflows/demultiplex.nf +++ b/workflows/demultiplex.nf @@ -66,6 +66,8 @@ workflow DEMULTIPLEX { ch_file_schema_validator = params.file_schema_validator ? Channel.fromPath(params.file_schema_validator, checkIfExists: true) : [] // file schema.json // Remove adapter from Illumina samplesheet to avoid adapter trimming in demultiplexer tools + ch_samplesheet = ch_samplesheet + .map{ meta, csv, tar, optional -> [[id: meta.id.toString(), lane: meta.lane], csv, tar, optional] } // Make meta.id be always a string if (params.remove_adapter && (params.demultiplexer in ["bcl2fastq", "bclconvert", "mkfastq"])) { ch_samplesheet_no_adapter = ch_samplesheet .collectFile(storeDir: "${params.outdir}") { item -> @@ -75,7 +77,7 @@ workflow DEMULTIPLEX { .map { file -> //build meta again from file name def meta_id = (file =~ /.*\/(.*?)(\.lane|_no_adapters)/)[0][1] //extracts everything from the last "/" until ".lane" or "_no_adapters" def meta_lane = (file.getName().contains('.lane')) ? (file =~ /\.lane(\d+)/)[0][1].toInteger() : null //extracts number after ".lane" until next "_", must be int to match lane value from meta - [ [id: meta_id, lane: meta_lane], file ] + [ [id: meta_id.toString(), lane: meta_lane], file ] // Make meta.id be always a string } ch_samplesheet_new = ch_samplesheet .join( ch_samplesheet_no_adapter, failOnMismatch: true ) From 68776c6cd76778a0a8eee08ea3ffb06072280527 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 21 Nov 2024 18:25:54 +0000 Subject: [PATCH 05/17] test: load test profile configs first --- nextflow.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/nextflow.config b/nextflow.config index 47cc7705..6d8aa62c 100755 --- a/nextflow.config +++ b/nextflow.config @@ -193,6 +193,12 @@ profiles { } +// Load base.config by default for all pipelines +includeConfig 'conf/base.config' + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + // Load nf-core custom profiles from different Institutions includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" From e8e1815e50774ee3189804b49a34e055b85aef4e Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 21 Nov 2024 18:34:40 +0000 Subject: [PATCH 06/17] Revert "test: load test profile configs first" This reverts commit 68776c6cd76778a0a8eee08ea3ffb06072280527. --- nextflow.config | 6 ------ 1 file changed, 6 deletions(-) diff --git a/nextflow.config b/nextflow.config index 6d8aa62c..47cc7705 100755 --- a/nextflow.config +++ b/nextflow.config @@ -193,12 +193,6 @@ profiles { } -// Load base.config by default for all pipelines -includeConfig 'conf/base.config' - -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' - // Load nf-core custom profiles from different Institutions includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" From 66a07db02fea51005bb305d832ff5a4a929c3dd8 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 21 Nov 2024 19:10:23 +0000 Subject: [PATCH 07/17] tests: update tests --- tests/bases2fastq.nf.test.snap | 8 +++--- tests/bcl2fastq.nf.test.snap | 8 +++--- tests/bclconvert.nf.test.snap | 8 +++--- tests/bclconvert_mini.nf.test.snap | 8 +++--- tests/fqtk.nf.test.snap | 8 +++--- tests/kraken.nf.test.snap | 8 +++--- tests/mkfastq.nf.test.snap | 8 +++--- tests/sgdemux.nf.test.snap | 8 +++--- tests/skip_tools.nf.test.snap | 40 +++++++++++++++--------------- tests/test_pe.nf.test.snap | 8 +++--- 10 files changed, 56 insertions(+), 56 deletions(-) diff --git a/tests/bases2fastq.nf.test.snap b/tests/bases2fastq.nf.test.snap index 0d02d50a..752388c9 100644 --- a/tests/bases2fastq.nf.test.snap +++ b/tests/bases2fastq.nf.test.snap @@ -19,7 +19,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -206,10 +206,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:03:45.396019249" + "timestamp": "2024-11-21T18:42:11.374939945" }, "rnaseq_samplesheet": { "content": [ diff --git a/tests/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap index f4dc5379..dc5154c7 100644 --- a/tests/bcl2fastq.nf.test.snap +++ b/tests/bcl2fastq.nf.test.snap @@ -36,7 +36,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -256,10 +256,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:05:10.862707812" + "timestamp": "2024-11-21T18:44:03.754694052" }, "taxprofiler_samplesheet": { "content": [ diff --git a/tests/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap index b4159002..7ab5c079 100644 --- a/tests/bclconvert.nf.test.snap +++ b/tests/bclconvert.nf.test.snap @@ -26,7 +26,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -242,10 +242,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:06:40.844267965" + "timestamp": "2024-11-21T18:45:41.681049213" }, "atacseq_samplesheet": { "content": [ diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index 8c6c27f5..374fd25e 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -26,7 +26,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -350,10 +350,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:09:33.510548826" + "timestamp": "2024-11-21T18:49:10.86724814" }, "atacseq_samplesheet": { "content": [ diff --git a/tests/fqtk.nf.test.snap b/tests/fqtk.nf.test.snap index 9654f26b..3aff9501 100644 --- a/tests/fqtk.nf.test.snap +++ b/tests/fqtk.nf.test.snap @@ -22,7 +22,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -803,10 +803,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:12:13.420210238" + "timestamp": "2024-11-21T18:52:14.140745818" }, "rnaseq_samplesheet": { "content": [ diff --git a/tests/kraken.nf.test.snap b/tests/kraken.nf.test.snap index 7d333dd5..5c1b890e 100644 --- a/tests/kraken.nf.test.snap +++ b/tests/kraken.nf.test.snap @@ -30,7 +30,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -264,10 +264,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:13:52.447688832" + "timestamp": "2024-11-21T18:54:14.349973051" }, "atacseq_samplesheet": { "content": [ diff --git a/tests/mkfastq.nf.test.snap b/tests/mkfastq.nf.test.snap index b9fbce79..278f50e8 100644 --- a/tests/mkfastq.nf.test.snap +++ b/tests/mkfastq.nf.test.snap @@ -16,7 +16,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -198,10 +198,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:16:10.021030199" + "timestamp": "2024-11-21T18:56:58.036201181" }, "rnaseq_samplesheet": { "content": [ diff --git a/tests/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap index 4bb1d806..82488360 100644 --- a/tests/sgdemux.nf.test.snap +++ b/tests/sgdemux.nf.test.snap @@ -29,7 +29,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -613,10 +613,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:17:55.775005215" + "timestamp": "2024-11-21T18:58:50.931803001" }, "atacseq_samplesheet": { "content": [ diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap index 11d1c5ea..af1fc82b 100644 --- a/tests/skip_tools.nf.test.snap +++ b/tests/skip_tools.nf.test.snap @@ -13,7 +13,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -185,10 +185,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:19:55.20106833" + "timestamp": "2024-11-21T19:01:00.766139602" }, "rnaseq_samplesheet": { "content": [ @@ -217,7 +217,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -431,10 +431,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:19:14.365042" + "timestamp": "2024-11-21T19:00:16.803505471" }, "Skip MultiQC": { "content": [ @@ -453,7 +453,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -528,10 +528,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:23:16.963681621" + "timestamp": "2024-11-21T19:04:48.811944071" }, "atacseq_samplesheet": { "content": [ @@ -557,7 +557,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -729,10 +729,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:22:04.618283549" + "timestamp": "2024-11-21T19:03:31.839655727" }, "Skip Fastqc": { "content": [ @@ -751,7 +751,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -967,10 +967,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:21:16.816355313" + "timestamp": "2024-11-21T19:02:38.043654338" }, "taxprofiler_samplesheet": { "content": [ diff --git a/tests/test_pe.nf.test.snap b/tests/test_pe.nf.test.snap index 97a065bc..9bebeac8 100644 --- a/tests/test_pe.nf.test.snap +++ b/tests/test_pe.nf.test.snap @@ -36,7 +36,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3" + "nf-core/demultiplex": "v1.5.3dev" } }, [ @@ -339,10 +339,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-11-04T22:25:46.595698154" + "timestamp": "2024-11-21T19:07:38.034440806" }, "taxprofiler_samplesheet": { "content": [ From 46fc312398f8f19832229a7518d1b966cb309ee9 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 21 Nov 2024 19:12:47 +0000 Subject: [PATCH 08/17] test: add modules config afterwards to solve pass ext.args correctly in samshee --- conf/test_full.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/test_full.config b/conf/test_full.config index d591fdc4..33a5447b 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -19,3 +19,6 @@ params { demultiplexer = 'bcl2fastq' v1_schema = true } + +// Load modules.config afterwards to load ext.args in samshee correctly +includeConfig 'modules.config' From 28cd3dbd7f2e91e818b2a31ad46082030b4f2142 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 22 Nov 2024 09:51:53 +0000 Subject: [PATCH 09/17] test: include samshee config only for correct v1_schema --- conf/test_full.config | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index 33a5447b..b68526e8 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -21,4 +21,18 @@ params { } // Load modules.config afterwards to load ext.args in samshee correctly -includeConfig 'modules.config' +process { + withName: SAMSHEE { + ext.args = [ + params.json_schema_validator ? "--schema '${params.json_schema_validator}'" : "", + params.name_schema_validator ? "--schema '${params.name_schema_validator}'" : "", + params.v1_schema ? "--output-format sectioned" : "", + ].join(" ").trim() + errorStrategy = "terminate" + publishDir = [ + path: { "${params.outdir}/" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} From 751badd7e9cb8e81301dd1b56c3a02aabe63be86 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 Nov 2024 14:07:46 +0000 Subject: [PATCH 10/17] Bump samshee --- modules.json | 2 +- modules/nf-core/samshee/environment.yml | 2 +- modules/nf-core/samshee/main.nf | 4 ++-- modules/nf-core/samshee/tests/main.nf.test.snap | 14 +++++++------- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/modules.json b/modules.json index 326a8259..37cba9f5 100644 --- a/modules.json +++ b/modules.json @@ -67,7 +67,7 @@ }, "samshee": { "branch": "master", - "git_sha": "467c202a876d26af544fa8c4b22a050a535462a7", + "git_sha": "61e2a514b2ee26847d960386431b593a3c7d094f", "installed_by": ["modules"] }, "seqtk/sample": { diff --git a/modules/nf-core/samshee/environment.yml b/modules/nf-core/samshee/environment.yml index 35a8e2e7..09203856 100644 --- a/modules/nf-core/samshee/environment.yml +++ b/modules/nf-core/samshee/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samshee=0.2.1 + - bioconda::samshee=0.2.3 - python=3.13.0 diff --git a/modules/nf-core/samshee/main.nf b/modules/nf-core/samshee/main.nf index 6d7ba2e6..d40885c4 100644 --- a/modules/nf-core/samshee/main.nf +++ b/modules/nf-core/samshee/main.nf @@ -4,8 +4,8 @@ process SAMSHEE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/65/659cdc3068a6fbce17ccb199bb3afc8600c65940743c1a0214b3bf0eed4df1a3/data' : - 'community.wave.seqera.io/library/pip_samshee:9b655e3c18eee356' }" + 'oras://community.wave.seqera.io/library/pip_samshee:6ef3bad21377d60e' : + 'community.wave.seqera.io/library/pip_samshee:9a11bec0d7c8df27' }" input: tuple val(meta), path(samplesheet) diff --git a/modules/nf-core/samshee/tests/main.nf.test.snap b/modules/nf-core/samshee/tests/main.nf.test.snap index b3729eba..823dc3b0 100644 --- a/modules/nf-core/samshee/tests/main.nf.test.snap +++ b/modules/nf-core/samshee/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + "versions.yml:md5,cbbf34760bb4db290b14d619e7844f0e" ], "samplesheet": [ [ @@ -24,7 +24,7 @@ ] ], "versions": [ - "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + "versions.yml:md5,cbbf34760bb4db290b14d619e7844f0e" ] } ], @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + "versions.yml:md5,cbbf34760bb4db290b14d619e7844f0e" ], "samplesheet": [ [ @@ -59,7 +59,7 @@ ] ], "versions": [ - "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + "versions.yml:md5,cbbf34760bb4db290b14d619e7844f0e" ] } ], @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + "versions.yml:md5,cbbf34760bb4db290b14d619e7844f0e" ], "samplesheet": [ [ @@ -94,7 +94,7 @@ ] ], "versions": [ - "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + "versions.yml:md5,cbbf34760bb4db290b14d619e7844f0e" ] } ], @@ -104,4 +104,4 @@ }, "timestamp": "2024-10-16T15:25:24.540910786" } -} \ No newline at end of file +} From cdb42c59f6242678646c4974a45c50ce42f62c8f Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 29 Nov 2024 09:39:26 +0000 Subject: [PATCH 11/17] Added latest version of samshee --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4b65bbc8..3ee828eb 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#291](https://github.com/nf-core/demultiplex/pull/291) Updated `samshee` module to the latest version + ### `Fixed` - [#288](https://github.com/nf-core/demultiplex/pull/288) Fix `test_full` by validating parameters in `lenientMode` and fix workflow megatest workflow dispatch. From 47a36c8d96e77f002df30c0f051f32776b98bf67 Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Tue, 3 Dec 2024 15:55:41 +0000 Subject: [PATCH 12/17] Fixed email --- CHANGELOG.md | 1 + .../utils_nfcore_demultiplex_pipeline/main.nf | 8 +++- .../nf-core/utils_nfcore_pipeline/main.nf | 39 +++++++++---------- 3 files changed, 27 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3ee828eb..e7e4e6aa 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - [#288](https://github.com/nf-core/demultiplex/pull/288) Fix `test_full` by validating parameters in `lenientMode` and fix workflow megatest workflow dispatch. +- [#293](https://github.com/nf-core/demultiplex/pull/293) Fix workflow.onComplete email sending feature. ## 1.5.3 - 2024-11-06 diff --git a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf index 35008413..e3608a91 100644 --- a/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf @@ -128,7 +128,13 @@ workflow PIPELINE_COMPLETION { // // Completion email and summary // + // We need to ensure that the multiqc_report is a value channel (DataflowVariable). + // Queue channels will not be available in the workflow.onComplete block. + def multiqc_reports = multiqc_report.toList() + workflow.onComplete { + assert multiqc_reports instanceof groovyx.gpars.dataflow.DataflowVariable : "Expected a value channel (DataflowVariable) for multiqc_reports inside workflow.onComplete block." + if (email || email_on_fail) { completionEmail( summary_params, @@ -137,7 +143,7 @@ workflow PIPELINE_COMPLETION { plaintext_email, outdir, monochrome_logs, - multiqc_report.toList() + multiqc_reports.getVal() ) } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 5cb7bafe..a294185c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -248,32 +248,30 @@ def logColours(monochrome_logs=true) { // // Attach the multiqc report to email // -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { +def getSingleReport(multiqc_reports) { + switch (multiqc_reports) { + case Path: + return multiqc_reports + case List: + switch (multiqc_reports.size()) { + case 0: + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + case 1: + return multiqc_reports.first() + default: log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") - } - mqc_report = mqc_report[0] + return multiqc_reports.first() } - } - } - catch (Exception all) { - if (multiqc_report) { - log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") - } + default: + return null } - return mqc_report } // // Construct and send completion email // -def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { - +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_reports=[]) { // Set up the e-mail variables def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { @@ -320,7 +318,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_reports) // Check if we are only sending emails on failure def email_address = email @@ -351,7 +349,8 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi if (email_address) { try { if (plaintext_email) { -new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } From 47759733568438198dccd81d05c9af3cbf381cea Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Tue, 3 Dec 2024 15:56:27 +0000 Subject: [PATCH 13/17] Fix changelog PR number --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e7e4e6aa..73f31481 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - [#288](https://github.com/nf-core/demultiplex/pull/288) Fix `test_full` by validating parameters in `lenientMode` and fix workflow megatest workflow dispatch. -- [#293](https://github.com/nf-core/demultiplex/pull/293) Fix workflow.onComplete email sending feature. +- [#294](https://github.com/nf-core/demultiplex/pull/294) Fix workflow.onComplete email sending feature. ## 1.5.3 - 2024-11-06 From f6022b5ab240d22ba2441278b3fee494f93e5e5e Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Tue, 3 Dec 2024 16:36:34 +0000 Subject: [PATCH 14/17] Updated utils_nfcore_pipeline subworkflow --- modules.json | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 56 +++---------------- .../tests/main.function.nf.test | 52 ----------------- .../tests/main.function.nf.test.snap | 30 ---------- 4 files changed, 9 insertions(+), 131 deletions(-) diff --git a/modules.json b/modules.json index 37cba9f5..c73432ce 100644 --- a/modules.json +++ b/modules.json @@ -106,7 +106,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", + "git_sha": "d588e574e40a8aeba3636e2b766358091bfa3aa0", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a294185c..c2926b4a 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) { } } -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - def manifest_doi = workflow.manifest.doi.tokenize(",") - // Handling multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - manifest_doi.each { doi_ref -> - temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // @@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) { return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // @@ -245,8 +203,7 @@ def logColours(monochrome_logs=true) { return colorcodes } -// -// Attach the multiqc report to email +// Return a single report from an object that may be a Path or List // def getSingleReport(multiqc_reports) { switch (multiqc_reports) { @@ -271,7 +228,8 @@ def getSingleReport(multiqc_reports) { // // Construct and send completion email // -def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_reports=[]) { +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { + // Set up the e-mail variables def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { @@ -318,7 +276,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = getSingleReport(multiqc_reports) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -338,7 +296,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) @@ -357,7 +315,9 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi ['sendmail', '-t'].execute() << sendmail_html log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") } - catch (Exception all) { + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index 1dc317f8..e43d208b 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -41,58 +41,6 @@ nextflow_function { } } - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { - - function "nfCoreLogo" - - when { - function { - """ - input[0] = false - """ - } - } - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function dashedLine") { - - function "dashedLine" - - when { - function { - """ - input[0] = false - """ - } - } - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - test("Test Function without logColours") { function "logColours" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 1037232c..02c67014 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -17,26 +17,6 @@ }, "timestamp": "2024-02-28T12:02:59.729647" }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:10.562934" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:07.019761" - }, "Test Function without logColours": { "content": [ { @@ -95,16 +75,6 @@ }, "timestamp": "2024-02-28T12:03:17.969323" }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:14.366181" - }, "Test Function with logColours": { "content": [ { From e88837b102948c786e05311077b02c6b8680ce2d Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Tue, 3 Dec 2024 17:05:19 +0000 Subject: [PATCH 15/17] Bump versions for 1.5.4 release --- CHANGELOG.md | 3 ++- assets/multiqc_config.yml | 4 +--- nextflow.config | 2 +- tests/bases2fastq.nf.test.snap | 4 ++-- tests/bcl2fastq.nf.test.snap | 4 ++-- tests/bclconvert.nf.test.snap | 4 ++-- tests/bclconvert_mini.nf.test.snap | 4 ++-- tests/fqtk.nf.test.snap | 4 ++-- tests/kraken.nf.test.snap | 4 ++-- tests/mkfastq.nf.test.snap | 4 ++-- tests/sgdemux.nf.test.snap | 4 ++-- tests/skip_tools.nf.test.snap | 12 ++++++------ tests/test_pe.nf.test.snap | 4 ++-- 13 files changed, 28 insertions(+), 29 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 73f31481..6a0a65f7 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,13 +3,14 @@ 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). -## dev - [unreleased] +## 1.5.4 - 2024-12-03 ### `Added` ### `Changed` - [#291](https://github.com/nf-core/demultiplex/pull/291) Updated `samshee` module to the latest version +- [#295](https://github.com/nf-core/demultiplex/pull/295) Bump to version 1.5.4. ### `Fixed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 42478dee..91ee936d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,5 @@ report_comment: > - This report has been generated by the nf-core/demultiplex - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/demultiplex report_section_order: "nf-core-demultiplex-methods-description": diff --git a/nextflow.config b/nextflow.config index 47cc7705..0d82db47 100755 --- a/nextflow.config +++ b/nextflow.config @@ -265,7 +265,7 @@ manifest { description = """Demultiplexing pipeline for Illumina sequencing data""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '1.5.3dev' + version = '1.5.4' doi = '10.5281/zenodo.7153103' } diff --git a/tests/bases2fastq.nf.test.snap b/tests/bases2fastq.nf.test.snap index 752388c9..88515332 100644 --- a/tests/bases2fastq.nf.test.snap +++ b/tests/bases2fastq.nf.test.snap @@ -19,7 +19,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -241,4 +241,4 @@ }, "timestamp": "2024-10-30T15:25:57.12531458" } -} \ No newline at end of file +} diff --git a/tests/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap index dc5154c7..bd981a68 100644 --- a/tests/bcl2fastq.nf.test.snap +++ b/tests/bcl2fastq.nf.test.snap @@ -36,7 +36,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -271,4 +271,4 @@ }, "timestamp": "2024-10-30T15:27:23.563785123" } -} \ No newline at end of file +} diff --git a/tests/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap index 7ab5c079..f98058b6 100644 --- a/tests/bclconvert.nf.test.snap +++ b/tests/bclconvert.nf.test.snap @@ -26,7 +26,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -267,4 +267,4 @@ }, "timestamp": "2024-10-30T15:28:53.253703589" } -} \ No newline at end of file +} diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index 374fd25e..04a0a1e7 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -26,7 +26,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -375,4 +375,4 @@ }, "timestamp": "2024-10-30T15:34:31.69965379" } -} \ No newline at end of file +} diff --git a/tests/fqtk.nf.test.snap b/tests/fqtk.nf.test.snap index 3aff9501..d5dfbb3f 100644 --- a/tests/fqtk.nf.test.snap +++ b/tests/fqtk.nf.test.snap @@ -22,7 +22,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -838,4 +838,4 @@ }, "timestamp": "2024-10-30T15:37:11.05337654" } -} \ No newline at end of file +} diff --git a/tests/kraken.nf.test.snap b/tests/kraken.nf.test.snap index 5c1b890e..50956176 100644 --- a/tests/kraken.nf.test.snap +++ b/tests/kraken.nf.test.snap @@ -30,7 +30,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -289,4 +289,4 @@ }, "timestamp": "2024-10-30T15:38:42.216897057" } -} \ No newline at end of file +} diff --git a/tests/mkfastq.nf.test.snap b/tests/mkfastq.nf.test.snap index 278f50e8..a75ef853 100644 --- a/tests/mkfastq.nf.test.snap +++ b/tests/mkfastq.nf.test.snap @@ -16,7 +16,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -233,4 +233,4 @@ }, "timestamp": "2024-10-30T15:40:24.166541035" } -} \ No newline at end of file +} diff --git a/tests/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap index 82488360..dfa9e6c8 100644 --- a/tests/sgdemux.nf.test.snap +++ b/tests/sgdemux.nf.test.snap @@ -29,7 +29,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -638,4 +638,4 @@ }, "timestamp": "2024-10-30T15:42:08.908513986" } -} \ No newline at end of file +} diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap index af1fc82b..89d83f3c 100644 --- a/tests/skip_tools.nf.test.snap +++ b/tests/skip_tools.nf.test.snap @@ -13,7 +13,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -217,7 +217,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -453,7 +453,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -557,7 +557,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -751,7 +751,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -982,4 +982,4 @@ }, "timestamp": "2024-10-30T15:59:51.098330417" } -} \ No newline at end of file +} diff --git a/tests/test_pe.nf.test.snap b/tests/test_pe.nf.test.snap index 9bebeac8..50986705 100644 --- a/tests/test_pe.nf.test.snap +++ b/tests/test_pe.nf.test.snap @@ -36,7 +36,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.3dev" + "nf-core/demultiplex": "v1.5.4dev" } }, [ @@ -354,4 +354,4 @@ }, "timestamp": "2024-10-30T15:50:01.08084426" } -} \ No newline at end of file +} From 7fe86df69d3b20aac872311c40f696b3178c6b2b Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Tue, 3 Dec 2024 17:48:36 +0000 Subject: [PATCH 16/17] Update versions --- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 +++- tests/bases2fastq.nf.test.snap | 2 +- tests/bcl2fastq.nf.test.snap | 2 +- tests/bclconvert.nf.test.snap | 2 +- tests/bclconvert_mini.nf.test.snap | 2 +- tests/fqtk.nf.test.snap | 2 +- tests/kraken.nf.test.snap | 2 +- tests/mkfastq.nf.test.snap | 2 +- tests/sgdemux.nf.test.snap | 2 +- tests/skip_tools.nf.test.snap | 10 +++++----- tests/test_pe.nf.test.snap | 2 +- 12 files changed, 18 insertions(+), 16 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a0a65f7..6aa846fb 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - [#291](https://github.com/nf-core/demultiplex/pull/291) Updated `samshee` module to the latest version -- [#295](https://github.com/nf-core/demultiplex/pull/295) Bump to version 1.5.4. +- [#296](https://github.com/nf-core/demultiplex/pull/296) Bump to version 1.5.4. ### `Fixed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 91ee936d..f2757d90 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,7 @@ report_comment: > - This report has been generated by the nf-core/demultiplex + This report has been generated by the nf-core/demultiplex + analysis pipeline. For information about how to interpret these results, please see the + documentation. report_section_order: "nf-core-demultiplex-methods-description": diff --git a/tests/bases2fastq.nf.test.snap b/tests/bases2fastq.nf.test.snap index 88515332..e5d7ccbb 100644 --- a/tests/bases2fastq.nf.test.snap +++ b/tests/bases2fastq.nf.test.snap @@ -19,7 +19,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ diff --git a/tests/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap index bd981a68..16c2b153 100644 --- a/tests/bcl2fastq.nf.test.snap +++ b/tests/bcl2fastq.nf.test.snap @@ -36,7 +36,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ diff --git a/tests/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap index f98058b6..a91be822 100644 --- a/tests/bclconvert.nf.test.snap +++ b/tests/bclconvert.nf.test.snap @@ -26,7 +26,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index 04a0a1e7..117f97cb 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -26,7 +26,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ diff --git a/tests/fqtk.nf.test.snap b/tests/fqtk.nf.test.snap index d5dfbb3f..337817b4 100644 --- a/tests/fqtk.nf.test.snap +++ b/tests/fqtk.nf.test.snap @@ -22,7 +22,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ diff --git a/tests/kraken.nf.test.snap b/tests/kraken.nf.test.snap index 50956176..2c576172 100644 --- a/tests/kraken.nf.test.snap +++ b/tests/kraken.nf.test.snap @@ -30,7 +30,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ diff --git a/tests/mkfastq.nf.test.snap b/tests/mkfastq.nf.test.snap index a75ef853..3ddf421a 100644 --- a/tests/mkfastq.nf.test.snap +++ b/tests/mkfastq.nf.test.snap @@ -16,7 +16,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ diff --git a/tests/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap index dfa9e6c8..db5e55a0 100644 --- a/tests/sgdemux.nf.test.snap +++ b/tests/sgdemux.nf.test.snap @@ -29,7 +29,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap index 89d83f3c..2442f45c 100644 --- a/tests/skip_tools.nf.test.snap +++ b/tests/skip_tools.nf.test.snap @@ -13,7 +13,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ @@ -217,7 +217,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ @@ -453,7 +453,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ @@ -557,7 +557,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ @@ -751,7 +751,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ diff --git a/tests/test_pe.nf.test.snap b/tests/test_pe.nf.test.snap index 50986705..81ae7e84 100644 --- a/tests/test_pe.nf.test.snap +++ b/tests/test_pe.nf.test.snap @@ -36,7 +36,7 @@ "md5sum": 8.3 }, "Workflow": { - "nf-core/demultiplex": "v1.5.4dev" + "nf-core/demultiplex": "v1.5.4" } }, [ From 50193d82f48979461eb0fc861fe3c44ae84bdacd Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Fri, 6 Dec 2024 13:46:47 +0000 Subject: [PATCH 17/17] bump version in .nf-core.tml --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index e679aab8..e79022c8 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -17,5 +17,5 @@ template: outdir: . skip_features: - igenomes - version: 1.5.3dev + version: 1.5.4 update: null