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Added IRIDA Next JSON output file #10

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merged 1 commit into from
Jun 10, 2024
Merged

Added IRIDA Next JSON output file #10

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19 changes: 19 additions & 0 deletions conf/iridanext.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
iridanext {
enabled = true
output {
path = "${params.outdir}/iridanext.output.json.gz"
overwrite = true
files {
global = [
]
samples = [
"**/**/detailed_summary.tsv",
"**/**/mlst.tsv",
"**/**/plasmidfinder.tsv",
"**/**/resfinder.tsv",
"**/**/results.xlsx",
"**/**/settings.txt",
"**/**/summary.tsv"]
}
}
}
5 changes: 5 additions & 0 deletions nextflow.config
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Expand Up @@ -179,8 +179,10 @@ singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
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Could you change nf-validation to [email protected] so that we are using a fixed version.

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Will do!

id '[email protected]' // Output for IRIDA Next
}


// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
Expand All @@ -191,6 +193,9 @@ if (!params.igenomes_ignore) {
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

// Config file for nf-iridanext
includeConfig 'conf/iridanext.config'

env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
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