diff --git a/workflows/epigenetics/atacseq/atacseq.ga b/workflows/epigenetics/atacseq/atacseq.ga index 664948390d..43920b558e 100644 --- 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 -} \ No newline at end of file +} 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 index 1e5edfc2fa..32a7a248e1 100644 --- 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 -} \ No newline at end of file +} diff --git a/workflows/epigenetics/chipseq-pe/chipseq-pe.ga b/workflows/epigenetics/chipseq-pe/chipseq-pe.ga index d2790c1195..b5b597d602 100644 --- 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 -} \ No newline at end of file +} diff --git a/workflows/epigenetics/chipseq-sr/chipseq-sr.ga b/workflows/epigenetics/chipseq-sr/chipseq-sr.ga index 4c3b60c6c7..34fd800064 100644 --- 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 -} \ No newline at end of file +} diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga index 6a069cc8e7..88b45e1c5c 100644 --- 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 -} \ No newline at end of file +} diff --git a/workflows/epigenetics/cutandrun/cutandrun.ga b/workflows/epigenetics/cutandrun/cutandrun.ga index 5f8a1fcb6f..50bf65b33f 100644 --- 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 -} \ No newline at end of file +} 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 index 903a8e783d..9f9d7b432f 100644 --- 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 index 71ea93dc91..c1990e9576 100644 --- 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 -} \ No newline at end of file +}