updating readmes to explain more what to trying workflow mean

galaxyproject · Jun 19, 2024 · 2b5eced · 2b5eced
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Showing 17 changed files with 11 additions and 11 deletions.
diff --git a/...ed-pathogen-identification/.dockstore.yml → ...ed-pathogen-identification/.dockstore.yml b/...ed-pathogen-identification/.dockstore.yml → ...ed-pathogen-identification/.dockstore.yml
diff --git a/...e-based-Pathogen-Identification-tests.yml → ...e-based-Pathogen-Identification-tests.yml b/...e-based-Pathogen-Identification-tests.yml → ...e-based-Pathogen-Identification-tests.yml
diff --git a/...n/Allele-based-Pathogen-Identification.ga → ...n/Allele-based-Pathogen-Identification.ga b/...n/Allele-based-Pathogen-Identification.ga → ...n/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/...ased-pathogen-identification/CHANGELOG.md → ...ased-pathogen-identification/CHANGELOG.md b/...ased-pathogen-identification/CHANGELOG.md → ...ased-pathogen-identification/CHANGELOG.md
@@ -1,5 +1,5 @@
 # Changelog
 
-## [0.1] 2023-08-08
+## [0.1] 2024-06-19
 
 First release.
diff --git a/...e-based-pathogen-identification/README.md → ...e-based-pathogen-identification/README.md b/...e-based-pathogen-identification/README.md → ...e-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/...ata/mapping_mean_depth_per_sample.tabular → ...ata/mapping_mean_depth_per_sample.tabular b/...ata/mapping_mean_depth_per_sample.tabular → ...ata/mapping_mean_depth_per_sample.tabular
diff --git a/...amples_Spike3bBarcode10.fastq.gz.fastq.gz → ...amples_Spike3bBarcode10.fastq.gz.fastq.gz b/...amples_Spike3bBarcode10.fastq.gz.fastq.gz → ...amples_Spike3bBarcode10.fastq.gz.fastq.gz
diff --git a/...amples_Spike3bBarcode12.fastq.gz.fastq.gz → ...amples_Spike3bBarcode12.fastq.gz.fastq.gz b/...amples_Spike3bBarcode12.fastq.gz.fastq.gz → ...amples_Spike3bBarcode12.fastq.gz.fastq.gz
diff --git a/...eference_genome_of_tested_strain.fasta.gz → ...eference_genome_of_tested_strain.fasta.gz b/...eference_genome_of_tested_strain.fasta.gz → ...eference_genome_of_tested_strain.fasta.gz
diff --git a/...flows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga b/...flows/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
@@ -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
@@ -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
@@ -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/...-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga b/...-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/...e/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/README.md b/...e/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
@@ -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/...profiling-and-visualization-with-krona/Taxonomy-Profiling-and-Visualization-with-Krona.ga b/...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"
         },
         {