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Removing ArborView as a Parameter for Azure Compatibility #11

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May 14, 2024
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4 changes: 0 additions & 4 deletions nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -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"
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22 changes: 3 additions & 19 deletions nextflow_schema.json
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -354,9 +341,6 @@
{
"$ref": "#/definitions/gas_cluster"
},
{
"$ref": "#/definitions/arborview"
},
{
"$ref": "#/definitions/institutional_config_options"
},
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1 change: 0 additions & 1 deletion tests/nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion workflows/gasclustering.nf
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Looks good! I assume the projectDir variable is fine in azure?

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Yes, it should. It's the directory containing the main script: https://www.nextflow.io/docs/latest/script.html#script-implicit-variables

Original file line number Diff line number Diff line change
Expand Up @@ -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 (
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