diff --git a/CHANGELOG.md b/CHANGELOG.md index f598c69..a991091 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). -## [v1.1.0dev] +## v1.1.0dev - [date] ## [v1.0.1](https://github.com/nf-core/reportho/releases/tag/1.0.1) [2024-06-14] diff --git a/CITATIONS.md b/CITATIONS.md index 5c5643e..e785f87 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -56,6 +56,10 @@ > Vincent Lefort, Richard Desper, Olivier Gascuel, FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program, Molecular Biology and Evolution, Volume 32, Issue 10, October 2015, Pages 2798–2800, https://doi.org/10.1093/molbev/msv150 +- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) diff --git a/conf/test.config b/conf/test.config index 444087a..bcbe957 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,7 +23,7 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - input = pipelines_testdata_base_path + 'reportho/testdata/samplesheet/samplesheet.csv' + input = params.pipelines_testdata_base_path + 'reportho/testdata/samplesheet/samplesheet.csv' // Other parameters skip_eggnog = true diff --git a/conf/test_full.config b/conf/test_full.config index 3102d69..a35bf07 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,7 +15,7 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data - input = pipelines_testdata_base_path + 'reportho/testdata/samplesheet/samplesheet.csv' + input = params.pipelines_testdata_base_path + 'reportho/testdata/samplesheet/samplesheet.csv' // Other parameters eggnog_path = 'http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/1/1_members.tsv.gz' diff --git a/modules.json b/modules.json index 4d23f74..0ccf3ca 100644 --- a/modules.json +++ b/modules.json @@ -41,12 +41,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb", + "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb", + "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/nextflow.config b/nextflow.config index e553bda..358268f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -295,5 +295,41 @@ validation { } } +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + +validation { + defaultIgnoreParams = ["genomes"] + help { + enabled = true + command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + beforeText = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m ${manifest.name} ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/${manifest.name}/blob/master/CITATIONS.md +""" + } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText + } +} + // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' diff --git a/subworkflows/local/utils_nfcore_reportho_pipeline/main.nf b/subworkflows/local/utils_nfcore_reportho_pipeline/main.nf index 2856e46..fbfe276 100644 --- a/subworkflows/local/utils_nfcore_reportho_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_reportho_pipeline/main.nf @@ -187,32 +187,6 @@ def validateInputSamplesheet(input) { return input } -// -// Get attribute from genome config file e.g. fasta -// -def getGenomeAttribute(attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null -} - -// -// Exit pipeline if incorrect --genome key provided -// -def genomeExistsError() { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - error(error_string) - } -} - // // Generate methods description for MultiQC // @@ -222,7 +196,6 @@ def toolCitationText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", - "FastQC (Andrews 2010),", "MultiQC (Ewels et al. 2016)", "." ].join(' ').trim() @@ -235,7 +208,6 @@ def toolBibliographyText() { // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " ].join(' ').trim() diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 4d7f09c..2b0dc67 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 805dcc4..b78273c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // diff --git a/workflows/reportho.nf b/workflows/reportho.nf index 26e4f68..904d740 100644 --- a/workflows/reportho.nf +++ b/workflows/reportho.nf @@ -147,8 +147,12 @@ workflow REPORTHO { // Collate and save software versions // softwareVersionsToYAML(ch_versions) - .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) - .set { ch_collated_versions } + .collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', + sort: true, + newLine: true + ).set { ch_collated_versions } //