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FEAT: UPPMAX Claim profile responsibility + add rnaseq config #1097

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FEAT: UPPMAX Claim profile responsibility + add rnaseq config #1097

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3a28f01
Claim profile responsibility
maxulysse Apr 22, 2026
6ea3f98
add rnaseq pipeline UPPMAX specific config
maxulysse Apr 22, 2026
bb78983
first POC
maxulysse Apr 23, 2026
a5fc841
include params file for pico
maxulysse Apr 23, 2026
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22 changes: 22 additions & 0 deletions conf/pipeline/rnaseq/uppmax.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
params {
// Add a description only if the NGI_CONFIG environment variable is set
// which only happens on prod on miarka
config_profile_description = System.getenv('NGI_CONFIG')
? 'nf-core/rnaseq UPPMAX cluster profile provided by nf-core/configs.'
: 'UPPMAX (Bianca) cluster profile provided by nf-core/configs.'
Comment on lines +4 to +6
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@pontus pontus Apr 27, 2026

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Don't we need to keep these in closures with .call()


// Overrides default values when genome is GRCh38
gencode = (System.getenv('NGI_CONFIG') && params.genome == 'GRCh38')
save_reference = (System.getenv('NGI_CONFIG') && params.genome == 'GRCh38')

genomes {
'GRCh38' {
bed12 = System.getenv('NGI_CONFIG')
? "/proj/ngi2016003/nobackup/junw/RNAseq/genes_GRCh38.bed"
: "/sw/data/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
gtf = System.getenv('NGI_CONFIG')
? "/sw/data/uppnex/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf"
: "/sw/data/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
}
}
}
2 changes: 1 addition & 1 deletion conf/uppmax.config
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Expand Up @@ -10,7 +10,7 @@
params {
// Description is overwritten for other clusters using includeConfig
config_profile_description = 'UPPMAX (Bianca) cluster profile provided by nf-core/configs.'
config_profile_contact = 'Phil Ewels (@ewels)'
config_profile_contact = 'Maxime Garcia (@maxulysse)'
config_profile_url = 'https://www.uppmax.uu.se/'
project = null
clusterOptions = null
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3 changes: 3 additions & 0 deletions pipeline/rnaseq.config
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Expand Up @@ -15,6 +15,9 @@ profiles {
eddie {
includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config"
}
uppmax {
includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/uppmax.config"
}
utd_sysbio {
includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/utd_sysbio.config"
}
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