From c3f1adf09b9c933494621355e27ef378a30f1a07 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 13 Mar 2023 12:13:17 +0100 Subject: [PATCH 1/6] First release Zenodo update --- README.md | 5 ++--- lib/WorkflowMain.groovy | 5 ++--- nextflow.config | 2 +- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index ba08835..29fcd31 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_light.png#gh-light-mode-only) ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_dark.png#gh-dark-mode-only) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7728364-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7728364) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) @@ -98,8 +98,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - - +If you use nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.5281/zenodo.7728364](https://doi.org/10.5281/zenodo.7728364) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index b343e83..24511f6 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -9,9 +9,8 @@ class WorkflowMain { // public static String citation(workflow) { return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - // TODO nf-core: Add Zenodo DOI for pipeline after first release - //"* The pipeline\n" + - //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + + "* The pipeline\n" + + " https://doi.org/10.5281/zenodo.7728364\n\n" + '* The nf-core framework\n' + ' https://doi.org/10.1038/s41587-020-0439-x\n\n' + '* Software dependencies\n' + diff --git a/nextflow.config b/nextflow.config index 80038ea..3d745e4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -306,7 +306,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' version = '1.0.0' - doi = '' + doi = '10.5281/zenodo.7728364' } // Load modules.config for DSL2 module specific options From 982fba1b5849f458806ad0ef10afc5fdc33807ef Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 11 May 2023 14:13:18 +0200 Subject: [PATCH 2/6] Fix taxpasta not receiving taxonomy directory --- CHANGELOG.md | 12 ++++++++++++ conf/modules.config | 1 - subworkflows/local/standardisation_profiles.nf | 2 +- 3 files changed, 13 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c055527..9858ab9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,18 @@ 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). +## v1.0.1 - Dodgy Dachshund Patch [2023-05-11] + +### `Added` + +### `Fixed` + +- [#291](https://github.com/nf-core/taxprofiler/pull/291) - Fix Taxpasta not receiving taxonomy directory (❤️ to SannaAb for reporting, fix by @jfy133) + +### `Dependencies` + +### `Deprecated` + ## v1.0.0 - Dodgy Dachshund [2023-03-13] Initial release of nf-core/taxprofiler, created with the [nf-core](https://nf-co.re/) template. diff --git a/conf/modules.config b/conf/modules.config index ee1a3d2..301ec9a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -543,7 +543,6 @@ process { ext.args = { [ "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}", - params.taxpasta_taxonomy_dir ? "--taxonomy ${params.taxpasta_taxonomy_dir}" : "", params.taxpasta_add_name ? "--add-name" : "", params.taxpasta_add_rank ? "--add-rank" : "", params.taxpasta_add_lineage ? "--add-lineage" : "", diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf index 26355b7..dde76c8 100644 --- a/subworkflows/local/standardisation_profiles.nf +++ b/subworkflows/local/standardisation_profiles.nf @@ -33,7 +33,7 @@ workflow STANDARDISATION_PROFILES { .groupTuple () .map { [ it[0], it[1].flatten() ] } - TAXPASTA_MERGE (ch_input_for_taxpasta, [], []) + TAXPASTA_MERGE (ch_input_for_taxpasta, params.taxpasta_taxonomy_dir ? params.taxpasta_taxonomy_dir : [], []) /* Split profile results based on tool they come from From c0897ecc78ef1cd7b18bc4d2b9e45c05d33b72cf Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 11 May 2023 14:14:18 +0200 Subject: [PATCH 3/6] Bump version to 1.0.1 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 3d745e4..74476fe 100644 --- a/nextflow.config +++ b/nextflow.config @@ -305,7 +305,7 @@ manifest { description = """Taxonomic classification and profiling of shotgun metagenomic data""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0.0' + version = '1.0.1' doi = '10.5281/zenodo.7728364' } From e8b85d0b62a8dce012e8eaa45df7df8c88522b34 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 11 May 2023 14:19:50 +0200 Subject: [PATCH 4/6] Update nextflow.config Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 74476fe..d8af1d1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -305,7 +305,7 @@ manifest { description = """Taxonomic classification and profiling of shotgun metagenomic data""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0.1' + version = '1.0.1' doi = '10.5281/zenodo.7728364' } From 5d95151f549713bcdf9b59aa44768a4b2b39e0b2 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 11 May 2023 15:04:37 +0200 Subject: [PATCH 5/6] Fix staging --- subworkflows/local/standardisation_profiles.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf index dde76c8..4ae44fd 100644 --- a/subworkflows/local/standardisation_profiles.nf +++ b/subworkflows/local/standardisation_profiles.nf @@ -33,7 +33,9 @@ workflow STANDARDISATION_PROFILES { .groupTuple () .map { [ it[0], it[1].flatten() ] } - TAXPASTA_MERGE (ch_input_for_taxpasta, params.taxpasta_taxonomy_dir ? params.taxpasta_taxonomy_dir : [], []) + ch_taxpasta_tax_dir = params.taxpasta_taxonomy_dir ? Channel.fromPath(params.taxpasta_taxonomy_dir, checkIfExists: true).collect() : [] + + TAXPASTA_MERGE (ch_input_for_taxpasta, ch_taxpasta_tax_dir, []) /* Split profile results based on tool they come from From 8ff8ab8b70c53cdf64f16dee5ffffbb257cadd24 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 15 May 2023 09:27:35 +0200 Subject: [PATCH 6/6] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9858ab9..884dcdb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v1.0.1 - Dodgy Dachshund Patch [2023-05-11] +## v1.0.1 - Dodgy Dachshund Patch [2023-05-15] ### `Added`