diff --git a/nextflow.config b/nextflow.config index 2ab8af5..8cfac84 100644 --- a/nextflow.config +++ b/nextflow.config @@ -60,10 +60,6 @@ params { gm_thresholds = "10,5,0" gm_delimiter = "." - // Arborview specific data - // TODO check this works in azure - av_html = "./assets/ArborView.html" - // Metadata metadata_1_header = "metadata_1" metadata_2_header = "metadata_2" diff --git a/nextflow_schema.json b/nextflow_schema.json index 91e6710..e05e9af 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -120,15 +120,15 @@ }, "pd_missing_threshold": { "type": "number", - "default": 1 + "default": 1.0 }, "pd_sample_quality_threshold": { "type": "number", - "default": 1 + "default": 1.0 }, "pd_match_threshold": { "type": "number", - "default": -1 + "default": -1.0 }, "pd_file_type": { "type": "string", @@ -174,19 +174,6 @@ } } }, - "arborview": { - "title": "ArborView", - "type": "object", - "description": "", - "default": "", - "properties": { - "av_html": { - "type": "string", - "default": "./assets/ArborView.html", - "hidden": true - } - } - }, "institutional_config_options": { "title": "Institutional config options", "type": "object", @@ -354,9 +341,6 @@ { "$ref": "#/definitions/gas_cluster" }, - { - "$ref": "#/definitions/arborview" - }, { "$ref": "#/definitions/institutional_config_options" }, diff --git a/tests/nextflow.config b/tests/nextflow.config index 3ad9843..1c6d7b9 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -6,7 +6,6 @@ params.max_memory = "2.GB" params.max_cpus = 1 -params.av_html = "$baseDir/assets/ArborView.html" /* This is required to run in WSL/Ubuntu using singularity Without this, profile_dists was not successfully completing diff --git a/workflows/gasclustering.nf b/workflows/gasclustering.nf index bcc350a..fd84e66 100644 --- a/workflows/gasclustering.nf +++ b/workflows/gasclustering.nf @@ -121,7 +121,7 @@ workflow GASCLUSTERING { data_and_metadata = APPEND_METADATA(clustered_data.clusters, metadata_rows, metadata_headers) tree_data = clustered_data.tree.merge(data_and_metadata) // mergeing as no key to join on - tree_html = file(params.av_html) + tree_html = file("$projectDir/assets/ArborView.html") ARBOR_VIEW(tree_data, tree_html) CUSTOM_DUMPSOFTWAREVERSIONS (