Annotate all existing WFs with edam topics and operations

workflows/amplicon/dada2/dada2_paired.ga

@@ -15,6 +15,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "dada2 amplicon analysis pipeline - for paired end data",
+    "edam_topics": ["topic_3837"],  # Metagenomic sequencing
+    "edam_operations": ["operation_3218", "operation_3219", "operation_3460", "operation_3798"],  # Sequencing quality control, Read pre-processing, Taxonomic classification, Read binning
     "release": "0.2",
     "steps": {
         "0": {
@@ -853,4 +855,4 @@
     ],
     "uuid": "11d717f8-92ef-4dd7-bda7-c193175fece2",
     "version": 1
-}
+}

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga

@@ -17,6 +17,8 @@
     "license": "MIT",
     "release": "0.3",
     "name": "QIIME2 Ia: multiplexed data (single-end)",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_2409", "operation_3933"],  # Data handling, Demultiplexing
     "steps": {
         "0": {
             "annotation": "Single-end sequences",

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga

@@ -17,6 +17,8 @@
     "license": "MIT",
     "release": "0.3",
     "name": "QIIME2 Ib: multiplexed data (paired-end)",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_2409", "operation_3933"],  # Data handling, Demultiplexing
     "steps": {
         "0": {
             "annotation": "All the forward-directed FASTQ sequences",
@@ -443,4 +445,4 @@
     "tags": [],
     "uuid": "b09b5420-bb7c-4f27-9c90-7e2031889379",
     "version": 49
-}
+}

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ic-demultiplexed-data-single-end.ga

@@ -17,6 +17,8 @@
     "license": "MIT",
     "release": "0.3",
     "name": "QIIME2 Ic: Demultiplexed data (single-end)",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_2409"],  # Data handling
     "steps": {
         "0": {
             "annotation": "A collection of single-end demultiplexed sequences",
@@ -287,4 +289,4 @@
     "tags": [],
     "uuid": "5a57f873-52f8-4c51-9e8d-e747d32d183a",
     "version": 1
-}
+}

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end.ga

@@ -17,6 +17,8 @@
     "release": "0.3",
     "license": "MIT",
     "name": "QIIME2 Id: Demultiplexed data (paired-end)",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_2409"],  # Data handling
     "steps": {
         "0": {
             "annotation": "Import of the paired-end demultiplexed sequences",
@@ -275,4 +277,4 @@
     "tags": [],
     "uuid": "f4887024-6f68-4d53-a889-5635366dd18d",
     "version": 2
-}
+}

workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga

@@ -18,6 +18,8 @@
     "release": "0.3",
     "license": "MIT",
     "name": "QIIME2 IIa: Denoising (sequence quality control) and feature table creation (single-end)",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_3219", "operation_3798"],  # Read pre-processing, Read binning
     "steps": {
         "0": {
             "annotation": "Tab separated metadata file",
@@ -375,4 +377,4 @@
     "tags": [],
     "uuid": "718df5b9-9cbb-4792-be50-604e18ef0548",
     "version": 2
-}
+}

workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga

@@ -18,6 +18,8 @@
     "release": "0.3",
     "license": "MIT",
     "name": "QIIME2 IIb: Denoising (sequence quality control) and feature table creation (paired-end)",
+    "edam_topics": ["topic_3168", "topic_3301"],  # Sequencing, Microbiology
+    "edam_operations": ["operation_3219", "operation_3798"],  # Read pre-processing, Read binning
     "steps": {
         "0": {
             "annotation": "Tab separated metadata file",
@@ -441,4 +443,4 @@
     "tags": [],
     "uuid": "8b8c4f4c-7cc0-422d-9a6f-47357faa0082",
     "version": 1
-}
+}

workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga

@@ -17,6 +17,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis",
+    "edam_topics": ["topic_3168", "topic_3837"],  # Microbiology, Metagenomic sequencing
+    "edam_operations": ["operation_0540", "operation_3460"],  # Phylogenetic inference (from molecular sequences), Taxonomic classification
     "release": "0.2",
     "steps": {
         "0": {
@@ -1075,4 +1077,4 @@
     "tags": [],
     "uuid": "3163175d-7673-42d9-8aae-505afbd74946",
     "version": 30
-}
+}

workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga

@@ -121,6 +121,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "QIIME2 VI: Diversity metrics and estimations",
+    "edam_topics": ["topic_3168", "topic_3837"],  # Microbiology, Metagenomic sequencing
+    "edam_operations": ["operation_0289", "operation_3658"],  # Sequence distance matrix generation, Statistical inference
     "release": "0.2",
     "steps": {
         "0": {
@@ -1129,4 +1131,4 @@
     "tags": [],
     "uuid": "300b5a7d-f763-486a-a8ea-87ea84571f19",
     "version": 2
-}
+}

workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga

@@ -29,6 +29,8 @@
     "license": "GPL-3.0-or-later",
     "release": "1.1.5",
     "name": "amr_gene_detection",
+    "edam_topics": ["topic_0080", "topic_3301"],  # Sequence analysis, Microbiology
+    "edam_operations": ["operation_3461", "operation_3482", "operation_3840"],  # Virulence prediction, Antimicrobial resistance prediction, Multilocus sequence typing
     "steps": {
         "0": {
             "annotation": "Can be any fasta file.",
@@ -692,4 +694,4 @@
     ],
     "uuid": "dfcedd6a-9dc1-4dcd-8b15-dbd21482f463",
     "version": 1
-}
+}

workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga

@@ -29,6 +29,8 @@
     "license": "GPL-3.0-or-later",
     "release": "1.1.7",
     "name": "bacterial_genome_annotation",
+    "edam_topics": ["topic_0080", "topic_3301"],  # Sequence analysis, Microbiology
+    "edam_operations": ["operation_2454", "operation_3918"],  # Gene prediction, Genome analysis
     "steps": {
         "0": {
             "annotation": "Can be any fasta file.",
@@ -1211,4 +1213,4 @@
     ],
     "uuid": "d55a9e46-a205-4143-b92f-3783499063ed",
     "version": 1
-}
+}

workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring.ga

@@ -16,6 +16,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "Fragment-based virtual screening using rDock for docking and SuCOS for pose scoring",
+    "edam_topics": ["topic_2258", "topic_3343"],  # Cheminformatics, Compound libraries and screening
+    "edam_operations": ["operation_0482"],  # Protein-ligand docking
     "release": "0.1.5",
     "steps": {
         "0": {

workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd.ga

@@ -11,6 +11,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "dcTMD calculations with GROMACS",
+    "edam_topics": ["topic_0176", "topic_2258"],  # Cheminformatics, Molecular dynamics
+    "edam_operations": ["operation_2476"],  # Molecular dynamics
     "release": "0.1.5",
     "steps": {
         "0": {
@@ -2229,4 +2231,4 @@
     "tags": [],
     "uuid": "7950b716-2bc9-4cb6-8472-6506c702adea",
     "version": 1
-}
+}

workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa.ga

@@ -11,6 +11,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "MMGBSA calculations with GROMACS",
+    "edam_topics": ["topic_0176", "topic_2258"],  # Cheminformatics, Molecular dynamics
+    "edam_operations": ["operation_2476"],  # Molecular dynamics
     "release": "0.1.5",
     "steps": {
         "0": {
@@ -1975,4 +1977,4 @@
     "tags": [],
     "uuid": "16455667-cdef-4979-9603-f338e09aa2a1",
     "version": 1
-}
+}

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
-}
+}

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
-}
+}

workflows/epigenetics/atacseq/atacseq.ga

@@ -13,6 +13,8 @@
     "license": "MIT",
     "release": "1.0",
     "name": "ATACseq",
+    "edam_topics": ["topic_3168", "topic_3173", "topic_3940"],  # Sequencing, Epigenomics, Chromosome conformation capture
+    "edam_categories": ["operation_3198", "operation_3219", "operation_3222"],  # Read mapping, Read pre-processing, Peak calling
     "steps": {
         "0": {
             "annotation": "Should be a paired collection with ATAC-seq fastqs",
@@ -1706,4 +1708,4 @@
     ],
     "uuid": "747f2432-7493-44b8-a5ee-82d104407cad",
     "version": 1
-}
+}

workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates.ga

@@ -12,6 +12,8 @@
     "license": "MIT",
     "release": "0.2",
     "name": "Average Bigwig between replicates",
+    "edam_topics": ["topic_3168"],  # Sequencing
+    "edam_operations": ["operation_3222", "operation_3230", "operation_3436"],  # Peak calling, Read depth analysis, Aggregation
     "steps": {
         "0": {
             "annotation": "We assume the identifiers are like:\nsample_name_replicateID",
@@ -164,4 +166,4 @@
     "tags": [],
     "uuid": "c6ed4b0e-d719-4997-9860-ba99488ec332",
     "version": 6
-}
+}

workflows/epigenetics/chipseq-pe/chipseq-pe.ga

@@ -12,6 +12,8 @@
     "license": "MIT",
     "release": "0.12",
     "name": "ChIPseq_PE",
+    "edam_topics": ["topic_3169", "topic_3173"],  # ChIP-seq, Epigenomics
+    "edam_categories": ["operation_3198", "operation_3219", "operation_3222"],  # Read mapping, Read pre-processing, Peak calling
     "steps": {
         "0": {
             "annotation": "Should be a paired collection with ChIPseq fastqs",
@@ -721,4 +723,4 @@
     ],
     "uuid": "1834d09c-c683-4424-bc8d-57df156c2fc8",
     "version": 1
-}
+}

workflows/epigenetics/chipseq-sr/chipseq-sr.ga

@@ -12,6 +12,8 @@
     "license": "MIT",
     "release": "0.12",
     "name": "ChIPseq_SR",
+    "edam_topics": ["topic_3169", "topic_3173"],  # ChIP-seq, Epigenomics
+    "edam_categories": ["operation_3198", "operation_3219", "operation_3222"],  # Read mapping, Read pre-processing, Peak calling
     "steps": {
         "0": {
             "annotation": "Should be a collection with ChIPseq fastqs",
@@ -690,4 +692,4 @@
     ],
     "uuid": "fe6bda9f-1fc2-4a86-bf8d-e779c79466fc",
     "version": 1
-}
+}

workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga

@@ -82,6 +82,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "release": "1.2",
+    "edam_topics": ["topic_3168"],  # Sequencing
+    "edam_operations": ["operation_3222", "operation_3230", "operation_3436"],  # Peak calling, Read depth analysis, Aggregation
     "name": "Get Confident Peaks From ChIP_PE replicates",
     "steps": {
         "0": {
@@ -1337,4 +1339,4 @@
     ],
     "uuid": "a2f66906-e9e3-42f9-8629-390017ed2db0",
     "version": 6
-}
+}

workflows/epigenetics/cutandrun/cutandrun.ga

@@ -12,6 +12,8 @@
     "license": "MIT",
     "release": "0.13",
     "name": "CUTandRUN",
+    "edam_topics": ["topic_3169", "topic_3173"],  # ChIP-seq, Epigenomics
+    "edam_categories": ["operation_3198", "operation_3219", "operation_3222"],  # Read mapping, Read pre-processing, Peak calling
     "steps": {
         "0": {
             "annotation": "Should be a paired collection with CUT and RUN fastqs",
@@ -845,4 +847,4 @@
     ],
     "uuid": "98e9e34b-b203-43db-9a23-5fa72963fa6d",
     "version": 1
-}
+}

workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga

@@ -12,6 +12,8 @@
     "license": "MIT",
     "release": "0.3",
     "name": "cHi-C_fastqToCool_hicup_cooler",
+    "edam_topics": ["topic_3168", "topic_3173", "topic_3940"],  # Sequencing, Epigenomics, Chromosome conformation capture
+    "edam_operations": ["operation_2442", "operation_3198"]  # DNA structure prediction, Read Mapping
     "steps": {
         "0": {
             "annotation": "Should be a paired collection with Hi-C fastqs",

workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga

@@ -12,6 +12,8 @@
     "license": "MIT",
     "release": "0.3",
     "name": "Hi-C_fastqToCool_hicup_cooler",
+    "edam_topics": ["topic_3168", "topic_3173", "topic_3940"],  # Sequencing, Epigenomics, Chromosome conformation capture
+    "edam_operations": ["operation_2442", "operation_3198"]  # DNA structure prediction, Read Mapping
     "steps": {
         "0": {
             "annotation": "Should be a paired collection with Hi-C fastqs",
@@ -1209,4 +1211,4 @@
     ],
     "uuid": "2196fbff-317e-437d-a022-696a1f95a850",
     "version": 4
-}
+}

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
-}
+}

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
-}
+}