Add edam terms for WFs from epigenetics folder

galaxyproject · Dec 17, 2024 · 3ba391b · 3ba391b
1 parent 8c091ad
commit 3ba391b
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Showing 8 changed files with 23 additions and 7 deletions.
diff --git a/workflows/epigenetics/atacseq/atacseq.ga b/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
-}
+}
diff --git a/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates.ga b/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
-}
+}
diff --git a/workflows/epigenetics/chipseq-pe/chipseq-pe.ga b/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
-}
+}
diff --git a/workflows/epigenetics/chipseq-sr/chipseq-sr.ga b/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
-}
+}
diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga b/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
-}
+}
diff --git a/workflows/epigenetics/cutandrun/cutandrun.ga b/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
-}
+}
diff --git a/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga b/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",

diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga b/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
-}
+}