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Nf annotation kegg viewer #164

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Nf annotation kegg viewer #164

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5768fc6
syntax fix and project code isolation testing
aw-watson Nov 5, 2025
c0995f1
publishing JSON for web viewer
aw-watson Nov 5, 2025
11b9fb0
Merge branch 'main' into nf-annotation-kegg-viewer
aw-watson Nov 5, 2025
0573a5a
correctly generating JSON data for annotation result charts
aw-watson Nov 19, 2025
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6 changes: 4 additions & 2 deletions workflows/Nextflow/modules/runAnnotation/runAnnotation.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -160,8 +160,8 @@ process keggPlots {
mode: 'copy'
)
publishDir(
path: "${settings["keggViewerDir"]}"
mode: 'copy'
path: "${settings["keggViewerDir"]}",
mode: 'copy',
pattern: "kegg_map/*"
)

Expand All @@ -172,11 +172,13 @@ process keggPlots {
output:
path "kegg_map/*"
path "kegg_map.log"
path "opaver_web_path.json"

script:
"""
check_server_up.pl --url "http://rest.kegg.jp" && \
opaver_anno.pl -g $gff -o ./kegg_map -p ${settings["projName"]} > kegg_map.log 2>&1
echo '{ "opaver_web_path":"opaver_web/pathway_anno.html?data=${settings["dataCode"]}" }' > opaver_web_path.json
"""
}

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1 change: 1 addition & 0 deletions workflows/Nextflow/nextflow.config
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Expand Up @@ -119,6 +119,7 @@ params {
gcode = null
keggView = false
keggViewerDir = "${projectDir}/../../../database/opaver_web/data/kegg_map"
dataCode = ""
}

binning {
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2 changes: 2 additions & 0 deletions workflows/Nextflow/templates/module_params.tmpl
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Expand Up @@ -86,6 +86,8 @@
gcode = <% if(typeof gcode !== 'undefined') { %><%= gcode %><% } else { %>11<%} %>
keggView = <% if(typeof keggView !== 'undefined') { %><%= keggView %><% } else { %>false<%} %>
keggViewerDir = <% if(typeof keggViewerDir !== 'undefined') { %>"<%= keggViewerDir %>"<% } else { %>"undefined"<%} %>
dataCode = "<%= nextflowOutDir %>".split("/")[-2]

}

binning {
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