FEAT: UPPMAX Claim profile responsibility + add rnaseq config

conf/pipeline/rnaseq/uppmax.config

@@ -0,0 +1,11 @@
+// NGI Stockholm specific configurations for rnaseq on UPPMAX (miarka)
+// Genome overrides are triggered by the SITE environment variable
+
+params {
+    config_profile_description = System.getenv('SITE') == 'NGI-S'
+        ? 'nf-core/rnaseq UPPMAX cluster profile provided by nf-core/configs.'
+        : 'UPPMAX (Bianca) cluster profile provided by nf-core/configs.'
+
+    gencode        = (System.getenv('SITE') == 'NGI-S' && params.genome == 'GRCh38')
+    save_reference = (System.getenv('SITE') == 'NGI-S' && params.genome == 'GRCh38')
+}

conf/pipeline/rnaseq/uppmax/rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml

@@ -0,0 +1,5 @@
+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"

conf/pipeline/rnaseq/uppmax/rnaseq_sthlm_params.yaml

@@ -0,0 +1,4 @@
+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"

conf/uppmax.config

@@ -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

docs/pipeline/rnaseq/uppmax.md

@@ -0,0 +1,28 @@
+# nf-core/configs: uppmax rnaseq specific configuration
+
+## NGI Stockholm specific configurations for uppmax
+
+When the `SITE` environment variable is set to `NGI-S` (as it is on production miarka in Stockholm), the following params are automatically set for the rnaseq pipeline when using `--genome GRCh38`:
+
+- `gencode = true`
+- `save_reference = true`
+
+Usage with nf-core/rnaseq:
+
+```bash
+nextflow run nf-core/rnaseq -profile uppmax --genome GRCh38 ...
+```
+
+### Params files
+
+Params files are available in `conf/pipeline/rnaseq/uppmax/`, both containing GRCh38 genome reference paths for bed12 and gtf files. They overwrite the genomes map from igenomes from GRCh38 and can then be used even when the `--genome` parameter is set to a different genome.
+
+`rnaseq_sthlm_params.yaml` only contains the genome reference paths, so optional when not using GRCh38.
+`rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml` is mandatory for Pico V3 library prep with UMIs, when using or not using the `--genome GRCh38` parameter.
+
+Example:
+
+```bash
+nextflow run nf-core/rnaseq -profile uppmax --genome GRCh38 \
+  -params-file conf/pipeline/rnaseq/uppmax/rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml
+```

pipeline/rnaseq.config

@@ -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"
     }