From 8c091ad19a91836875dbbf4b1e084b3b1292077c Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Tue, 17 Dec 2024 15:24:04 +0100
Subject: [PATCH] Annotate existing WFs with edam topics and operations

---
 .../parallel-accession-download.ga                            | 4 +++-
 .../sra-manifest-to-concatenated-fastqs.ga                    | 4 +++-
 .../assembly-with-flye/Genome-assembly-with-Flye.ga           | 4 +++-
 .../bacterial-genome-assembly/bacterial_genome_assembly.ga    | 4 +++-
 .../Assembly-polishing-with-long-reads.ga                     | 2 ++
 .../quality_and_contamination_control.ga                      | 4 +++-
 .../segmentation-and-counting.ga                              | 2 ++
 .../gcms-metams/Mass-spectrometry__GCMS-with-metaMS.ga        | 4 +++-
 .../Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga       | 2 ++
 .../Allele-based-Pathogen-Identification.ga                   | 4 +++-
 .../Gene-based-Pathogen-Identification.ga                     | 2 ++
 .../nanopore-pre-processing/Nanopore-Pre-Processing.ga        | 2 ++
 ...ection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga | 2 ++
 .../Taxonomy-Profiling-and-Visualization-with-Krona.ga        | 2 ++
 .../clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga | 2 ++
 .../clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga    | 2 ++
 workflows/repeatmasking/RepeatMasking-Workflow.ga             | 4 +++-
 .../consensus-from-variation.ga                               | 4 +++-
 .../sars-cov-2-variation-reporting/variation-reporting.ga     | 4 +++-
 workflows/transcriptomics/brew3r/BREW3R.ga                    | 4 +++-
 .../transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga | 4 +++-
 workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga              | 4 +++-
 .../virology/pox-virus-amplicon/pox-virus-half-genome.ga      | 2 ++
 23 files changed, 59 insertions(+), 13 deletions(-)

diff --git a/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga b/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga
index e2629e0f17..a405f60f96 100644
--- a/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga
+++ b/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga
@@ -18,6 +18,8 @@
     "license": "MIT",
     "release": "0.1.14",
     "name": "Parallel Accession Download",
+    "edam_topics": ["topic_3168"],  # Sequencing
+    "edam_operations": ["operation_2409", "operation_2422"],  # Data handling, Data retrieval
     "steps": {
         "0": {
             "annotation": "Text file containing run accessions (starting with SRR, ERR or DRR), one per line.",
@@ -271,4 +273,4 @@
     "tags": [],
     "uuid": "15c3229d-8786-457f-a020-7aa64c0cf6e8",
     "version": 10
-}
\ No newline at end of file
+}
diff --git a/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs.ga b/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs.ga
index 6a5ec350e0..465edbbdc9 100644
--- a/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs.ga
+++ b/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs.ga
@@ -22,6 +22,8 @@
     "release": "0.7",
     "license": "MIT",
     "name": "sra_manifest_to_concatenated_fastqs_parallel",
+    "edam_topics": ["topic_3168"],  # Sequencing
+    "edam_operations": ["operation_2409", "operation_2422"],  # Data handling, Data retrieval
     "steps": {
         "0": {
             "annotation": "Input tabular from SRA Run Selector or home made (First row needs to be a header)",
@@ -739,4 +741,4 @@
     "tags": [],
     "uuid": "363898af-e598-4f0e-abd9-e6ded395ce66",
     "version": 3
-}
\ No newline at end of file
+}
diff --git a/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye.ga b/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye.ga
index 2de7b57cd2..62307ec7c9 100644
--- a/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye.ga
+++ b/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye.ga
@@ -12,6 +12,8 @@
     "license": "MIT",
     "release": "0.2",
     "name": "Genome assembly with Flye",
+    "edam_topics": ["topic_0196"],  # Sequence assembly
+    "edam_operations": ["operation_0524", "operation_3180"],  # De-novo assembly, Sequence assembly validation
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n\n"
     },
@@ -262,4 +264,4 @@
     "tags": [],
     "uuid": "83ef6fdc-b8a9-41af-a824-0225f0199e63",
     "version": 21
-}
\ No newline at end of file
+}
diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
index be7a019c97..fd91ac033d 100644
--- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
+++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
@@ -29,6 +29,8 @@
     "release": "1.1.5",
     "license": "GPL-3.0-or-later",
     "name": "Bacterial Genome Assembly using Shovill",
+    "edam_topics": ["topic_0196", "topic_3301"],  # Sequence assembly, Microbiology
+    "edam_operations": ["operation_0524", "operation_3180"],  # De-novo assembly, Sequence assembly validation
     "steps": {
         "0": {
             "annotation": "Should be the adapter trimmed forward strand of the paired end reads.",
@@ -715,4 +717,4 @@
     ],
     "uuid": "bfe7f341-07ef-4bfe-9b50-2bc7628d6c55",
     "version": 1
-}
\ No newline at end of file
+}
diff --git a/workflows/genome-assembly/polish-with-long-reads/Assembly-polishing-with-long-reads.ga b/workflows/genome-assembly/polish-with-long-reads/Assembly-polishing-with-long-reads.ga
index a2d19082d3..21279b071b 100644
--- a/workflows/genome-assembly/polish-with-long-reads/Assembly-polishing-with-long-reads.ga
+++ b/workflows/genome-assembly/polish-with-long-reads/Assembly-polishing-with-long-reads.ga
@@ -12,6 +12,8 @@
     "release": "0.1",
     "license": "MIT",
     "name": "Assembly polishing with long reads",
+    "edam_topics": ["topic_0196"],  # Sequence assembly
+    "edam_operations": ["operation_2425"],  # Optimisation and refinement
     "steps": {
         "0": {
             "annotation": "",
diff --git a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga
index 4fceeb71e6..8f0da66c95 100644
--- a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga
+++ b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga
@@ -29,6 +29,8 @@
     "license": "GPL-3.0-or-later",
     "release": "1.1.6",
     "name": "Quality and Contamination Control For Genome Assembly",
+    "edam_topics": ["topic_0637", "topic_3168", "topic_3174"],  # Taxonomy, Sequencing, Metagenomics
+    "edam_operations": ["operation_3218", "operation_3460"],  # Sequencing quality control, Taxonomic classification
     "steps": {
         "0": {
             "annotation": "Should be the forward strand of the paired end reads.",
@@ -816,4 +818,4 @@
     ],
     "uuid": "eb1c667d-639d-4403-a2b4-1cb6683e0fa5",
     "version": 1
-}
\ No newline at end of file
+}
diff --git a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting.ga b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting.ga
index 2fb2796524..c4c96120e6 100644
--- a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting.ga
+++ b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting.ga
@@ -13,6 +13,8 @@
     "license": "MIT",
     "release": "0.2",
     "name": "Segmentation and counting of cell nuclei in fluorescence microscopy images",
+    "edam_topics": ["topic_3383"],  # Bioimaging
+    "edam_operations": ["operation_3443"],  # Image analysis
     "steps": {
         "0": {
             "annotation": "The fluorescence microscopy images to be segmented. Must be the single image channel, which contains the cell nuclei.",
diff --git a/workflows/metabomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS.ga b/workflows/metabomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS.ga
index 1c2ce685c7..65cd29db19 100644
--- a/workflows/metabomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS.ga
+++ b/workflows/metabomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS.ga
@@ -13,6 +13,8 @@
     "release": "0.1",
     "license": "MIT",
     "name": "Mass spectrometry: GCMS with metaMS",
+    "edam_topics": ["topic_3172"],  # Metabolomics
+    "edam_operations": ["operation_3628", "operation_3803"],  # Chromatographic alignment, Natural product identification
     "steps": {
         "0": {
             "annotation": "",
@@ -466,4 +468,4 @@
     ],
     "uuid": "a2b0d4f7-164c-40d3-ac34-f248db18bbef",
     "version": 2
-}
\ No newline at end of file
+}
diff --git a/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga b/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga
index 6d0e77f834..d82263c5eb 100644
--- a/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga
+++ b/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga
@@ -13,6 +13,8 @@
     "license": "MIT",
     "release": "1.0",
     "name": "Mass spectrometry: LC-MS preprocessing with XCMS",
+    "edam_topics": ["topic_3172"],  # Metabolomics
+    "edam_operations": ["operation_3628", "operation_3803"],  # Chromatographic alignment, Natural product identification
     "steps": {
         "0": {
             "annotation": "",
diff --git a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga
index 2ef573362d..22b8beeba0 100644
--- a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga
+++ b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga
@@ -102,6 +102,8 @@
     "license": "MIT",
     "release": "0.1.2",
     "name": "Allele-based Pathogen Identification",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_3198", "operation_3223"],  # Read mapping, Variant calling
     "report": {
         "markdown": "# Allele-based Pathogen Identification Workflow Report\nBelow are the results for the Allele based Pathogenic Identification Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nThe Perprocessing workflow main output (Collection of all samples reads after quality retaining and hosts filtering), and a FASTA file of the reference genome of the main Pathogen identified in the Gene based Pathogen Identification workflow, or per-known to the user.\n\n## Workflow Output: \n\n### All variants found per sample against the reference genome\n\n```galaxy\nhistory_dataset_display(output=\"extracted_fields_from_the_vcf_output\")\n```\n\n### Number of variants per sample\n\n```galaxy\nhistory_dataset_display(output=\"number_of_variants_per_sample\")\n```\n\n### Mapping mean depth of coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_mean_depth_per_sample\")\n```\n\n### Mapping breadth of coverage percentage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_coverage_percentage_per_sample\")\n```\n\n"
     },
@@ -1324,4 +1326,4 @@
     ],
     "uuid": "435875a1-72c4-4fda-8943-3a78f25c6574",
     "version": 72
-}
\ No newline at end of file
+}
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 8be13a1c85..bd739fa992 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
@@ -113,6 +113,8 @@
     "license": "MIT",
     "release": "0.1",
     "name": "Gene-based Pathogen Identification",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_0524", "operation_2425", "operation_3461", "operation_3482"],  # De-novo assembly, Optimisation and refinement, Virulence prediction, Antimicrobial resistance prediction
     "report": {
         "markdown": "# Gene-based Pathogen Identification Workflow Report\n\nBelow are the results for the Gene based Pathogen Identification Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nThe Perprocessing workflow main output (Collection of all samples reads after quality retaining and hosts filtering)\n\n## Workflow Output\n\n### Identified contigs per sample\n\n```galaxy\nhistory_dataset_display(output=\"contigs\")\n```\n\n### Identified pathogenic genes per sample\n\n```galaxy\nhistory_dataset_display(output=\"vfs\")\n```\n\n### Identified Antimicrobial Resistance genes per sample\n\n```galaxy\nhistory_dataset_display(output=\"amrs\")\n```\n"
     },
diff --git a/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga b/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga
index 986f020ed7..3337a6ce73 100644
--- a/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga
+++ b/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing.ga
@@ -194,6 +194,8 @@
     "license": "MIT",
     "release": "0.1",
     "name": "Nanopore Preprocessing",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_3218", "operation_3219"],  # Sequencing quality control, Read pre-processing
     "report": {
         "markdown": "# Nanopore - Preprocessing Workflow Report\nBelow are the results of the Preprocessing  Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nA collection of all sample reads (all in the same sequence file format, e.g.: Fastq, Fastq.gz, Fastqsanger, etc.)\n\n## Workflow Outputs\n\n### Multi QC Report of all samples before reads quality retaining\n\n```galaxy\nhistory_dataset_as_image(output=\"multiQC_html_report_before_preprocessing\")\n```\n### Multi QC Report of all samples after reads quality retaining\n\n```galaxy\nhistory_dataset_as_image(output=\"multiQC_html_report_after_preprocessing\")\n```\n\n### Table of the total number of reads and the number of host reads\n\n```galaxy\nhistory_dataset_display(output=\"removed_hosts_percentage_tabular\")\n```\n\n"
     },
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 02fa90d5ac..5d4baf77de 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
@@ -204,6 +204,8 @@
     "license": "MIT",
     "release": "0.1",
     "name": "Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_0566", "operation_3436", "operation_3731"],  # Sequence cluster visualisation, Aggregation, Sample comparison
     "report": {
         "markdown": "# Pathogen Detection - PathoGFAIR Samples Aggregation and Visualisation Workflow Report\nBelow are the results for the PathoGFAIR Samples Aggregation and Visualisation Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nTabular files and a FASTA file from the Gene-based Pathogen Identification workflow, four other tabular files from Nanopore Preprocessing and Nanopore - Allele-based Pathogen Identification workflow, and an optional Metadata tabular file with more sample information:\n\nFrom Gene-based Pathogenic Identification workflow: \n- contigs, FASTA file\n- VFs, Tabular file\n- vfs_of_genes_identified_by_vfdb, Tabular file\n- AMRs, Tabular file\n- amr_identified_by_ncbi, Tabular file\n\nFrom Nanopore - Allele bases Pathogen Identification workflow: \n- number_of_variants_per_sample, Tabular file\n- mapping_mean_depth_per_sample, Tabular file\n- mapping_coverage_percentage_per_sample, Tabular file\n\nFrom Nanopore Preprocessing: \n- removed_hosts_percentage_tabular, Tabular file\n\n## Some of the Workflow Outputs\n\n1- All Samples VFs Heatmap\n\n```galaxy\nhistory_dataset_as_image(output=\"heatmap_png\")\n```\n\n2- All samples phylogenetic tree VFs based\n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_vfs\")\n```\n\n3- All samples Phylogenetic tree AMR based \n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_amrs\")\n```\n\n4- Bar-plot for the Number of reads before host sequences removal and Number of found host reads per sample, performed in the Nanopore - Preprocessing workflow\n\n\n5- Barplot for the total number of removed host sequences per sample\n\n \n6- Barplot for the Mapping mean depth of coverage per sample\n\n\n6- Barplot for the Mapping breadth of coverage percentage per sample\n\n\n7- Barplot for the total number of complex variants and SNPs identified per sample\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n"
     },
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 1f160fbf85..090d3f27eb 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
@@ -66,6 +66,8 @@
     "license": "MIT",
     "release": "0.1",
     "name": "Taxonomy Profiling and Visualization with Krona",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology,
+    "edam_operations": ["operation_3460"],  # Taxonomic classification
     "report": {
         "markdown": "# Taxonomy Profiling and Visualisation with Krona Workflow Report\n\nIn this workflow you can identify your microbial community, but identifying all possible Taxon found in your samples, from the kingdom level down to the species level. In the application of the pathogen detection, this workflow gives an overview of the possible bacterial found in samples and what might be a possible suspect for pathogenicity.\n\nThe workflow uses Kraken2 tool and allow the user to choose any Kraken2 database or other added ones depending on the user application or the input samples. All Kraken2 tool databases are available in Galaxy. More description about these databases can be found [here](https://benlangmead.github.io/aws-indexes/k2). Other databases can be also added to the tool, just contact us anytime for that. We recommend using StandardPF database.\n\nVisualization is done using Krona Pie Chart, and you can replace it with any other tool. e.g. Phinch interactive tool, which is also available in Galaxy\n\n## Workflow Inputs:\n\nThe per-processing workflow main output (Collection of all samples reads after quality retaining and hosts filtering)\n\n## Workflow Outputs are:\n\n### Taxonomy Tabular Report\n\nThe report shows the abundance of every taxon from the kingdom level down to the species level\n\n```galaxy\nhistory_dataset_display(output=\"converted_kraken_report\")\n```\n\n### Taxonomy Profiling Visualization with Krona\nAn interactive Pie chart showing the different identified taxons along with their percentages, which is one of the ways to visualize the previous taxonomy tabular\n\n```galaxy\nhistory_dataset_as_image(output=\"krona_pie_chart\")\n```\n"
     },
diff --git a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga
index c7ada0e474..8ce52bf8e1 100644
--- a/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga
+++ b/workflows/proteomics/clinicalmp/clinicalmp-discovery/iwc-clinicalmp-discovery-workflow.ga
@@ -12,6 +12,8 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "name": "Clinical Metaproteomics Discovery Workflow",
+    "edam_topics": ["topic_0121",],  # Proteomics
+    "edam_operations": ["operation_3649"],  # Target-Decoy
     "release": "0.1",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
diff --git a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga
index 9021d3f8aa..8fda25130f 100644
--- a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga
+++ b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga
@@ -11,6 +11,8 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "name": "Clinical Metaproteomics Quantitation",
+    "edam_topics": ["topic_0121",],  # Proteomics
+    "edam_operations": ["operation_3630"],  # Protein quantification
     "release": "0.1",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
diff --git a/workflows/repeatmasking/RepeatMasking-Workflow.ga b/workflows/repeatmasking/RepeatMasking-Workflow.ga
index 2ebbefa8a9..b2b5366f02 100644
--- a/workflows/repeatmasking/RepeatMasking-Workflow.ga
+++ b/workflows/repeatmasking/RepeatMasking-Workflow.ga
@@ -5,6 +5,8 @@
     "license": "MIT",
     "release": "0.1",
     "name": "Repeat masking with RepeatModeler and RepeatMasker",
+    "edam_topics": ["topic_0157"],  # Sequence composition, complexity and repeats
+    "edam_operations": ["operation_0368", "operation_0379"],  # Sequence masking, Repeat sequence detection
     "creator": [
         {
             "class": "Person",
@@ -172,4 +174,4 @@
     "tags": [],
     "uuid": "f25be8fa-7823-456f-9707-a497703f48d7",
     "version": 0
-}
\ No newline at end of file
+}
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga
index 7d19751edd..f8e758df1f 100644
--- a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga
@@ -11,6 +11,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: consensus construction",
+    "edam_topics": ["topic_0781", "topic_3324"],  # Virology, Infectious disease
+    "edam_operations": ["operation_0448"],  # Sequence alignment analysis (conservation)
     "release": "0.4.2",
     "steps": {
         "0": {
@@ -1228,4 +1230,4 @@
         "covid19.galaxyproject.org"
     ],
     "uuid": "06dc40a7-99f2-4b3c-ae21-b3dcb239306f"
-}
\ No newline at end of file
+}
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga
index 10afce516f..df64a7102f 100644
--- a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga
@@ -11,6 +11,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis reporting",
+    "edam_topics": ["topic_0781", "topic_3324"],  # Virology, Infectious disease
+    "edam_operations": ["operation_0566", "operation_3436", "operation_3731"],  # Sequence cluster visualisation, Aggregation, Sample comparison
     "release": "0.3.4",
     "steps": {
         "0": {
@@ -1713,4 +1715,4 @@
         "covid19.galaxyproject.org"
     ],
     "uuid": "b08c744d-7c61-4b58-ac5f-4b5886c3c643"
-}
\ No newline at end of file
+}
diff --git a/workflows/transcriptomics/brew3r/BREW3R.ga b/workflows/transcriptomics/brew3r/BREW3R.ga
index 6f466b2c5d..8b611987dc 100644
--- a/workflows/transcriptomics/brew3r/BREW3R.ga
+++ b/workflows/transcriptomics/brew3r/BREW3R.ga
@@ -12,6 +12,8 @@
     "format-version": "0.1",
     "license": "GPL-3.0-or-later",
     "name": "BREW3R",
+    "edam_topics": ["topic_3308"],  # Transcriptomics
+    "edam_operations": ["operation_0362"],  # Genome annotation
     "release": "0.2",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -452,4 +454,4 @@
     "tags": [],
     "uuid": "ac8ef6cb-1621-4b73-9362-8a460ef3c3a2",
     "version": 1
-}
\ No newline at end of file
+}
diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga
index 9aa8986938..c1c937f647 100644
--- a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga
+++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga
@@ -13,6 +13,8 @@
     "license": "MIT",
     "release": "0.2",
     "name": "RNAseq_DE_filtering_plotting",
+    "edam_topics": ["topic_3308"],  # Transcriptomics
+    "edam_operations": ["operation_3223"],  # Differential gene expression profiling
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
     },
@@ -1131,4 +1133,4 @@
     ],
     "uuid": "15d188a7-b028-4cf7-bb5d-13858e1f6e78",
     "version": 15
-}
\ No newline at end of file
+}
diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga
index 2ca5955bb9..50f3583d29 100644
--- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga
+++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga
@@ -81,6 +81,8 @@
     "license": "MIT",
     "release": "1.1",
     "name": "RNA-seq for Paired-end fastqs",
+    "edam_topics": ["topic_3170", "topic_3308"],  # RNA-Seq, Transcriptomics
+    "edam_operations": ["operation_3198", "operation_3219"],  # Read mapping, Read pre-processing
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
     },
@@ -3411,4 +3413,4 @@
     ],
     "uuid": "5ab1d724-01d4-4673-a3c3-ae2bc944458f",
     "version": 1
-}
\ No newline at end of file
+}
diff --git a/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga b/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga
index fe2d9fcb74..842b9ea1e4 100644
--- a/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga
+++ b/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga
@@ -18,6 +18,8 @@
     "license": "MIT",
     "release": "0.2",
     "name": "Pox Virus Illumina Amplicon Workflow from half-genomes",
+    "edam_topics": ["topic_0781", "topic_3168", "topic_3324"],  # Virology, Sequencing, Infectious disease
+    "edam_operations": ["operation_0448", "operation_3198", "operation_3218", "operation_3923"],  # Sequence alignment analysis (conservation), Read mapping, Sequencing quality control, Genome resequencing
     "steps": {
         "0": {
             "annotation": "The viral reference sequence to map sequenced reads against",