From 2b5eced96c7d3e9e682139004ca9a17f4a82e200 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Wed, 19 Jun 2024 22:40:20 +0200 Subject: [PATCH] updating readmes to explain more what to trying workflow mean --- .../.dockstore.yml | 0 .../Allele-based-Pathogen-Identification-tests.yml | 0 .../Allele-based-Pathogen-Identification.ga | 2 +- .../CHANGELOG.md | 2 +- .../README.md | 2 +- .../test-data/mapping_mean_depth_per_sample.tabular | 0 ...f_all_samples_Spike3bBarcode10.fastq.gz.fastq.gz | Bin ...f_all_samples_Spike3bBarcode12.fastq.gz.fastq.gz | Bin .../reference_genome_of_tested_strain.fasta.gz | Bin .../Gene-based-Pathogen-Identification.ga | 2 +- .../gene-based-pathogen-identification/README.md | 2 +- .../Nanopore-Pre-Processing.ga | 2 +- .../microbiome/nanopore-pre-processing/README.md | 2 +- ...hoGFAIR-Samples-Aggregation-and-Visualisation.ga | 2 +- .../README.md | 2 +- .../README.md | 2 +- ...xonomy-Profiling-and-Visualization-with-Krona.ga | 2 +- 17 files changed, 11 insertions(+), 11 deletions(-) rename workflows/microbiome/{nanopore-allele-based-pathogen-identification => allele-based-pathogen-identification}/.dockstore.yml (100%) rename workflows/microbiome/{nanopore-allele-based-pathogen-identification => allele-based-pathogen-identification}/Allele-based-Pathogen-Identification-tests.yml (100%) rename workflows/microbiome/{nanopore-allele-based-pathogen-identification => allele-based-pathogen-identification}/Allele-based-Pathogen-Identification.ga (99%) rename workflows/microbiome/{nanopore-allele-based-pathogen-identification => allele-based-pathogen-identification}/CHANGELOG.md (59%) rename workflows/microbiome/{nanopore-allele-based-pathogen-identification => allele-based-pathogen-identification}/README.md (70%) rename workflows/microbiome/{nanopore-allele-based-pathogen-identification => allele-based-pathogen-identification}/test-data/mapping_mean_depth_per_sample.tabular (100%) rename workflows/microbiome/{nanopore-allele-based-pathogen-identification => allele-based-pathogen-identification}/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode10.fastq.gz.fastq.gz (100%) rename workflows/microbiome/{nanopore-allele-based-pathogen-identification => allele-based-pathogen-identification}/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode12.fastq.gz.fastq.gz (100%) rename workflows/microbiome/{nanopore-allele-based-pathogen-identification => allele-based-pathogen-identification}/test-data/reference_genome_of_tested_strain.fasta.gz (100%) diff --git a/workflows/microbiome/nanopore-allele-based-pathogen-identification/.dockstore.yml b/workflows/microbiome/allele-based-pathogen-identification/.dockstore.yml similarity index 100% rename from workflows/microbiome/nanopore-allele-based-pathogen-identification/.dockstore.yml rename to workflows/microbiome/allele-based-pathogen-identification/.dockstore.yml diff --git a/workflows/microbiome/nanopore-allele-based-pathogen-identification/Allele-based-Pathogen-Identification-tests.yml b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification-tests.yml similarity index 100% rename from workflows/microbiome/nanopore-allele-based-pathogen-identification/Allele-based-Pathogen-Identification-tests.yml rename to workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification-tests.yml diff --git a/workflows/microbiome/nanopore-allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga similarity index 99% rename from workflows/microbiome/nanopore-allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga rename to workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga index df0ee2575..c2884a2b9 100644 --- a/workflows/microbiome/nanopore-allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga +++ b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga @@ -89,7 +89,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "B\u00e9r\u00e9nice Batut", + "name": "Bérénice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { diff --git a/workflows/microbiome/nanopore-allele-based-pathogen-identification/CHANGELOG.md b/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md similarity index 59% rename from workflows/microbiome/nanopore-allele-based-pathogen-identification/CHANGELOG.md rename to workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md index 69d847367..90b294f63 100644 --- a/workflows/microbiome/nanopore-allele-based-pathogen-identification/CHANGELOG.md +++ b/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md @@ -1,5 +1,5 @@ # Changelog -## [0.1] 2023-08-08 +## [0.1] 2024-06-19 First release. diff --git a/workflows/microbiome/nanopore-allele-based-pathogen-identification/README.md b/workflows/microbiome/allele-based-pathogen-identification/README.md similarity index 70% rename from workflows/microbiome/nanopore-allele-based-pathogen-identification/README.md rename to workflows/microbiome/allele-based-pathogen-identification/README.md index dafd874e5..ae9b38ad6 100644 --- a/workflows/microbiome/nanopore-allele-based-pathogen-identification/README.md +++ b/workflows/microbiome/allele-based-pathogen-identification/README.md @@ -9,4 +9,4 @@ This workflow identifies pathogens using an allelic approach, detecting Single N ## Output Datasets - VCF files indicating identified variants and SNPs, BAM files with mapping results, and Tabular files with mapping depth and coverage calculations. -This workflow is available to try via our [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) +If you're unsure how to use this workflows, or if you want to see it in action with test datasets, it is included in our detailed training material for foodborne pathogen detection and tracking. You can find step-by-step instructions and practical examples in the following [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) diff --git a/workflows/microbiome/nanopore-allele-based-pathogen-identification/test-data/mapping_mean_depth_per_sample.tabular b/workflows/microbiome/allele-based-pathogen-identification/test-data/mapping_mean_depth_per_sample.tabular similarity index 100% rename from workflows/microbiome/nanopore-allele-based-pathogen-identification/test-data/mapping_mean_depth_per_sample.tabular rename to workflows/microbiome/allele-based-pathogen-identification/test-data/mapping_mean_depth_per_sample.tabular diff --git a/workflows/microbiome/nanopore-allele-based-pathogen-identification/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode10.fastq.gz.fastq.gz b/workflows/microbiome/allele-based-pathogen-identification/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode10.fastq.gz.fastq.gz similarity index 100% rename from workflows/microbiome/nanopore-allele-based-pathogen-identification/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode10.fastq.gz.fastq.gz rename to workflows/microbiome/allele-based-pathogen-identification/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode10.fastq.gz.fastq.gz diff --git a/workflows/microbiome/nanopore-allele-based-pathogen-identification/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode12.fastq.gz.fastq.gz b/workflows/microbiome/allele-based-pathogen-identification/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode12.fastq.gz.fastq.gz similarity index 100% rename from workflows/microbiome/nanopore-allele-based-pathogen-identification/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode12.fastq.gz.fastq.gz rename to workflows/microbiome/allele-based-pathogen-identification/test-data/nanopore_preprocessed_reads_collection_collection_of_all_samples_Spike3bBarcode12.fastq.gz.fastq.gz diff --git a/workflows/microbiome/nanopore-allele-based-pathogen-identification/test-data/reference_genome_of_tested_strain.fasta.gz b/workflows/microbiome/allele-based-pathogen-identification/test-data/reference_genome_of_tested_strain.fasta.gz similarity index 100% rename from workflows/microbiome/nanopore-allele-based-pathogen-identification/test-data/reference_genome_of_tested_strain.fasta.gz rename to workflows/microbiome/allele-based-pathogen-identification/test-data/reference_genome_of_tested_strain.fasta.gz diff --git a/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga index 4280e1f9a..5ff0fb3f1 100644 --- a/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga +++ b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga @@ -100,7 +100,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "B\u00e9r\u00e9nice Batut", + "name": "Bérénice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { diff --git a/workflows/microbiome/gene-based-pathogen-identification/README.md b/workflows/microbiome/gene-based-pathogen-identification/README.md index 8ee421087..74855cfc3 100644 --- a/workflows/microbiome/gene-based-pathogen-identification/README.md +++ b/workflows/microbiome/gene-based-pathogen-identification/README.md @@ -19,4 +19,4 @@ In this workflow we: ## Output Datasets - FASTA and Tabular files to track genes and visualise our pathogenic identification through out all samples. -This workflow is available to try via our [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) +If you're unsure how to use this workflows, or if you want to see it in action with test datasets, it is included in our detailed training material for foodborne pathogen detection and tracking. You can find step-by-step instructions and practical examples in the following [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) diff --git a/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga b/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga index b001e9a10..d20c390d7 100644 --- a/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga +++ b/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga @@ -175,7 +175,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "B\u00e9r\u00e9nice Batut", + "name": "Bérénice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { diff --git a/workflows/microbiome/nanopore-pre-processing/README.md b/workflows/microbiome/nanopore-pre-processing/README.md index 374373d5f..e53cd8f46 100644 --- a/workflows/microbiome/nanopore-pre-processing/README.md +++ b/workflows/microbiome/nanopore-pre-processing/README.md @@ -14,4 +14,4 @@ Generally, we are not interested in the host sequences, but rather only those or - Tables indicating total number of reads before and after host sequences trimming, and the host sequences percentages found in each sample. -This workflow is available to try via our [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) +If you're unsure how to use this workflows, or if you want to see it in action with test datasets, it is included in our detailed training material for foodborne pathogen detection and tracking. You can find step-by-step instructions and practical examples in the following [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) diff --git a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga index 7003d8a3d..983c6daa1 100644 --- a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga +++ b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga @@ -196,7 +196,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "B\u00e9r\u00e9nice Batut", + "name": "Bérénice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { diff --git a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/README.md b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/README.md index 191026cea..644a6e98e 100644 --- a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/README.md +++ b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/README.md @@ -8,4 +8,4 @@ In this workflow, we will aggregate results and use the results from 3 workflows With these types of visualisations, we can have an overview of all samples and the genes, but also how samples are related to each other, which common pathogenic genes they share. Given the time of the sampling and the location one can easily identify using these graphs, where and when the contamination has occurred among the different samples. -This workflow is available to try via our [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) +If you're unsure how to use this workflows, or if you want to see it in action with test datasets, it is included in our detailed training material for foodborne pathogen detection and tracking. You can find step-by-step instructions and practical examples in the following [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) diff --git a/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/README.md b/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/README.md index b1eb14b75..9330c2012 100644 --- a/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/README.md +++ b/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/README.md @@ -12,4 +12,4 @@ For taxonomy profiling Kraken2 tool is used along with one of its standard datab ## Output Datasets - Taxonomy profiling Tabular file, visualisation figures and interactive pie charts. -This workflow is available to try via our [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) +If you're unsure how to use this workflows, or if you want to see it in action with test datasets, it is included in our detailed training material for foodborne pathogen detection and tracking. You can find step-by-step instructions and practical examples in the following [GTN tutorial](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) diff --git a/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/Taxonomy-Profiling-and-Visualization-with-Krona.ga b/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/Taxonomy-Profiling-and-Visualization-with-Krona.ga index 79979a3c2..1f160fbf8 100644 --- a/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/Taxonomy-Profiling-and-Visualization-with-Krona.ga +++ b/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/Taxonomy-Profiling-and-Visualization-with-Krona.ga @@ -53,7 +53,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "B\u00e9r\u00e9nice Batut", + "name": "Bérénice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, {