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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
61b23ad
Merge branch 'master' into uppmax_miarka_rnaseq
maxulysse Jun 24, 2026
3dc18fb
simpler params files
maxulysse Jun 24, 2026
c276b76
add docs
maxulysse Jun 24, 2026
aa6378e
Finalize uppmax rnaseq configuration
maxulysse Jun 25, 2026
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7 changes: 7 additions & 0 deletions conf/pipeline/rnaseq/uppmax/rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml
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extra_trimgalore_args: "--clip_r2 14"
genomes:
GRCh38:
bed12: "/proj/ngi2016003/nobackup/junw/RNAseq/genes_GRCh38.bed"
gtf: "/sw/data/uppnex/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf"
gencode: true
save_reference: true
6 changes: 6 additions & 0 deletions conf/pipeline/rnaseq/uppmax/rnaseq_sthlm_params.yaml
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genomes:
GRCh38:
bed12: "/proj/ngi2016003/nobackup/junw/RNAseq/genes_GRCh38.bed"
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gtf: "/sw/data/uppnex/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf"
gencode: true
save_reference: true
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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10 changes: 10 additions & 0 deletions docs/pipeline/rnaseq/uppmax.md
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# nf-core/configs: uppmax rnaseq specific configuration

## NGI Stockholm specific configurations for uppmax

UPPMAX specific [parameter files](https://docs.seqera.io/nextflow/config#parameter-file) have been made for rnaseq, used by NGI Stockholm for their internal usage of the rnaseq pipeline.

Available params files in `conf/pipeline/rnaseq/uppmax/`:

- `rnaseq_sthlm_params.yaml` — GRCh38 genome reference paths (bed12, gtf) and gencode settings
- `rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml` — Same as above, with extra TrimGalore arguments (`--clip_r2 14`) for Pico V3 library prep with UMIs
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