FEAT: UPPMAX Claim profile responsibility + add rnaseq config

[maxulysse]

---

name: New Config
about: A new cluster config

Please follow these steps before submitting your PR:

• If your PR is a work in progress, include [WIP] in its title
• Your PR targets the master branch
• You've included links to relevant issues, if any

Steps for adding a new config profile:

• Add your custom config file to the conf/ directory
• Add your documentation file to the docs/ directory
• Add your custom profile to the nfcore_custom.config file in the top-level directory
• Add your profile name to the profile: scope in .github/workflows/main.yml
• OPTIONAL: Add your custom profile path and GitHub user name to .github/CODEOWNERS (**/<custom-profile>** @<github-username>)

[maxulysse]

export NXF_VER=25.10.2 ; nextflow run nf-core/rnaseq -r 3.12.0 -profile docker --outdir results -params-file /home/maxulysse/workspace/configs/conf/pipeline/rnaseq/uppmax/rnaseq_sthlm_params.yaml
[...]
 N E X T F L O W   ~  version 25.10.2

Launching `https://github.com/nf-core/rnaseq` [shrivelled_borg] DSL2 - revision: 3bec2331ca [3.12.0]
[...]
Reference genome options
  gencode        : true
  save_reference : true

export NXF_VER=25.10.2 ; nextflow run nf-core/rnaseq -r 3.12.0 -profile docker --outdir results -params-file /home/maxulysse/workspace/configs/conf/pipeline/rnaseq/uppmax/rnaseq_sthlm_params.yaml --genome GRCh38
[...]
 N E X T F L O W   ~  version 25.10.2

Launching `https://github.com/nf-core/rnaseq` [stoic_poisson] DSL2 - revision: 3bec2331ca [3.12.0]
[...]
Reference genome options
  genome         : GRCh38
  gtf            : /sw/data/uppnex/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf
  gene_bed       : /proj/ngi2016003/nobackup/junw/RNAseq/genes_GRCh38.bed
  gencode        : true
  save_reference : true

export NXF_VER=26.04.4 ; nextflow run nf-core/rnaseq -r 3.26.0 -profile docker --outdir results -params-file /home/maxulysse/workspace/configs/conf/pipeline/rnaseq/uppmax/rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml

 N E X T F L O W   ~  version 26.04.4

Launching `https://github.com/nf-core/rnaseq` [sick_yonath] revision: e7ca46272c [master]
[...]
Reference genome options
  gencode                                  : true

Read trimming options
  extra_trimgalore_args                    : --clip_r2 14
[...]
Optional outputs
  save_reference                           : true

export NXF_VER=26.04.4 ; nextflow run nf-core/rnaseq -r 3.26.0 -profile docker --outdir results -params-file /home/maxulysse/workspace/configs/conf/pipeline/rnaseq/uppmax/rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml --genome GRCh38

 N E X T F L O W   ~  version 26.04.4

Launching `https://github.com/nf-core/rnaseq` [thirsty_murdock] revision: e7ca46272c [master]
[...]
Reference genome options
  genome                                   : GRCh38
  fasta                                    : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
  gtf                                      : /sw/data/uppnex/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf
  gene_bed                                 : /proj/ngi2016003/nobackup/junw/RNAseq/genes_GRCh38.bed
  star_index                               : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/
  bowtie2_index                            : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/
  gencode                                  : true

Read trimming options
  extra_trimgalore_args                    : --clip_r2 14
[...]
Optional outputs
  save_reference                           : true