From f98f3c6c93824ddb79e15166fd857d249efbfc7f Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 14 Oct 2024 10:52:11 +1300 Subject: [PATCH 1/3] Version string --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index a379021..ec027f9 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -44,5 +44,5 @@ template: - igenomes - multiqc - fastqc - version: 2.2.0+dev + version: 2.2.0dev update: null From fec91354103a7555b7ac4e3d23e9236798e268f1 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 14 Oct 2024 11:02:11 +1300 Subject: [PATCH 2/3] Merge TEMPLATE version 3.0.2 --- .gitignore | 1 + .nf-core.yml | 8 +++---- CHANGELOG.md | 4 ++-- CITATION.cff | 2 +- modules.json | 4 ++-- nextflow.config | 2 +- .../utils_nfcore_assemblyqc_pipeline/main.nf | 9 +++----- .../nf-core/utils_nextflow_pipeline/main.nf | 22 ++++++++++--------- .../nf-core/utils_nfcore_pipeline/main.nf | 2 +- 9 files changed, 27 insertions(+), 27 deletions(-) diff --git a/.gitignore b/.gitignore index 837a2cd..3950461 100644 --- a/.gitignore +++ b/.gitignore @@ -14,3 +14,4 @@ testing* # nf-test files .nf-test/ .nf-test.log +null/ diff --git a/.nf-core.yml b/.nf-core.yml index ec027f9..3be9314 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,5 +1,8 @@ bump_version: null lint: + actions_ci: false + multiqc_config: false + template_strings: false files_exist: - conf/igenomes.config - conf/igenomes_ignored.config @@ -18,9 +21,6 @@ lint: - .github/workflows/branch.yml - .github/workflows/linting.yml - docs/README.md - multiqc_config: false - template_strings: false - actions_ci: false nextflow_config: - manifest.name - manifest.homePage @@ -28,7 +28,7 @@ lint: - validation.help.afterText - validation.summary.beforeText - validation.summary.afterText -nf_core_version: 3.0.1 +nf_core_version: 3.0.2 org_path: null repository_type: pipeline template: diff --git a/CHANGELOG.md b/CHANGELOG.md index 0ce92b0..d230856 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,12 +3,12 @@ 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). -## v2.2.0+dev - [10-Oct-2024] +## v2.2.0dev - [10-Oct-2024] ### `Added` 1. Added Gfastats [#126](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/126) -2. Updated nf-core/template to 3.0.1 [#149](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/149) +2. Updated nf-core/template to 3.0.2 [#149](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/149) 3. Updated `samtools faidx` to 1.21 4. Now using nf-test for pipeline level testing [#153](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/153) 5. Added `text/html` as content mime type for the report file [#146](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/146) diff --git a/CITATION.cff b/CITATION.cff index 3b342d8..37a9c84 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -25,7 +25,7 @@ authors: - family-names: "Deng" given-names: "Cecilia" title: "AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality" -version: 2.2.0+dev +version: 2.2.0dev date-released: 2024-07-30 url: "https://github.com/Plant-Food-Research-Open/assemblyqc" doi: 10.1093/bioinformatics/btae477 diff --git a/modules.json b/modules.json index f44be8f..a1a8360 100644 --- a/modules.json +++ b/modules.json @@ -281,12 +281,12 @@ }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/nextflow.config b/nextflow.config index 4adfe98..88134d2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -272,7 +272,7 @@ manifest { description = """A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '2.2.0+dev' + version = '2.2.0dev' doi = 'https://doi.org/10.1093/bioinformatics/btae477' } diff --git a/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf b/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf index 78ad703..d9fbc33 100644 --- a/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf @@ -49,7 +49,6 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) - // // Validate parameters and generate parameter summary to stdout // @@ -59,7 +58,6 @@ workflow PIPELINE_INITIALISATION { null // schema path: nextflow_schema ) - // // Check config provided to the pipeline // @@ -190,10 +188,9 @@ workflow PIPELINE_COMPLETION { take: email // string: email address email_on_fail // string: email address sent on pipeline failure - plaintext_email // boolean: Send plain-text email instead of HTML - - outdir // path: Path to output directory where results will be published - monochrome_logs // boolean: Disable ANSI colour codes in log output + plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published + monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 4d7f09c..0fcbf7b 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -106,17 +106,19 @@ def checkCondaChannels() { def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - - required_channels_in_order.eachWithIndex { channel, index -> - if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) - } - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn( - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - ) + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 805dcc4..5cb7baf 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) { def workflowCitation() { def temp_doi_ref = "" def manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + // 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 -> From 05b9eedac3310517ace080286d1653833f096e4f Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 14 Oct 2024 11:15:52 +1300 Subject: [PATCH 3/3] Updated snapshots --- .nf-core.yml | 1 + tests/hicparam/main.nf.test.snap | 4 ++-- tests/invalid/main.nf.test.snap | 4 ++-- tests/minimal/main.nf.test.snap | 2 +- tests/noltr/main.nf.test.snap | 4 ++-- tests/stub/main.nf.test.snap | 4 ++-- tests/tiny/main.nf.test.snap | 4 ++-- 7 files changed, 12 insertions(+), 11 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 3be9314..902fd78 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -16,6 +16,7 @@ lint: - .github/workflows/awsfulltest.yml files_unchanged: - LICENSE + - .gitignore - .github/CONTRIBUTING.md - .github/PULL_REQUEST_TEMPLATE.md - .github/workflows/branch.yml diff --git a/tests/hicparam/main.nf.test.snap b/tests/hicparam/main.nf.test.snap index 6ca72d8..feebbdb 100644 --- a/tests/hicparam/main.nf.test.snap +++ b/tests/hicparam/main.nf.test.snap @@ -68,7 +68,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0+dev" + "plant-food-research-open/assemblyqc": "v2.2.0dev" } }, "stable paths": [ @@ -99,4 +99,4 @@ }, "timestamp": "2024-10-10T16:11:00.660108" } -} \ No newline at end of file +} diff --git a/tests/invalid/main.nf.test.snap b/tests/invalid/main.nf.test.snap index bdd1665..9aa72f4 100644 --- a/tests/invalid/main.nf.test.snap +++ b/tests/invalid/main.nf.test.snap @@ -35,7 +35,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0+dev" + "plant-food-research-open/assemblyqc": "v2.2.0dev" } }, "stable paths": [ @@ -51,4 +51,4 @@ }, "timestamp": "2024-10-10T15:59:12.150838" } -} \ No newline at end of file +} diff --git a/tests/minimal/main.nf.test.snap b/tests/minimal/main.nf.test.snap index 7538396..44a5d9f 100644 --- a/tests/minimal/main.nf.test.snap +++ b/tests/minimal/main.nf.test.snap @@ -35,7 +35,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0+dev" + "plant-food-research-open/assemblyqc": "v2.2.0dev" } }, "stable paths": [ diff --git a/tests/noltr/main.nf.test.snap b/tests/noltr/main.nf.test.snap index 68b8513..75ee9f5 100644 --- a/tests/noltr/main.nf.test.snap +++ b/tests/noltr/main.nf.test.snap @@ -50,7 +50,7 @@ "seqkit": "v2.8.0" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0+dev" + "plant-food-research-open/assemblyqc": "v2.2.0dev" } }, "stable paths": [ @@ -84,4 +84,4 @@ }, "timestamp": "2024-10-10T20:38:08.028244" } -} \ No newline at end of file +} diff --git a/tests/stub/main.nf.test.snap b/tests/stub/main.nf.test.snap index 257765b..74b3740 100644 --- a/tests/stub/main.nf.test.snap +++ b/tests/stub/main.nf.test.snap @@ -230,7 +230,7 @@ "untar": 1.34 }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0+dev" + "plant-food-research-open/assemblyqc": "v2.2.0dev" } }, "stable paths": [ @@ -304,4 +304,4 @@ }, "timestamp": "2024-10-10T14:56:44.730644" } -} \ No newline at end of file +} diff --git a/tests/tiny/main.nf.test.snap b/tests/tiny/main.nf.test.snap index c3a241a..60dfdbb 100644 --- a/tests/tiny/main.nf.test.snap +++ b/tests/tiny/main.nf.test.snap @@ -29,7 +29,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0+dev" + "plant-food-research-open/assemblyqc": "v2.2.0dev" } }, "stable paths": [ @@ -44,4 +44,4 @@ }, "timestamp": "2024-10-10T14:46:59.600343" } -} \ No newline at end of file +}