Annotate more WFs

wm75 · Dec 18, 2024 · 1a54f57 · 1a54f57
1 parent 3ba391b
commit 1a54f57
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Showing 14 changed files with 40 additions and 12 deletions.
diff --git a/workflows/amplicon/dada2/dada2_paired.ga b/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
-}
+}
diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga b/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",

diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga b/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
-}
+}
diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ic-demultiplexed-data-single-end.ga b/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
-}
+}
diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end.ga b/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
-}
+}
diff --git a/.../qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga b/.../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
-}
+}
diff --git a/.../qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga b/.../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
-}
+}
diff --git a/...n/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga b/...n/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
-}
+}
diff --git a/...ws/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga b/...ws/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
-}
+}
diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga b/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
-}
+}
diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga b/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
-}
+}
diff --git a/.../computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring.ga b/.../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": {

diff --git a/workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd.ga b/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
-}
+}
diff --git a/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa.ga b/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
-}
+}