diff --git a/conf/pipeline/rnaseq/rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml b/conf/pipeline/rnaseq/rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml new file mode 100644 index 000000000..58306bfad --- /dev/null +++ b/conf/pipeline/rnaseq/rnaseq_sthlm_Pico-V3-trim_UMIs_params.yaml @@ -0,0 +1 @@ +extra_trimgalore_args: "--clip_r2 14" diff --git a/conf/pipeline/rnaseq/uppmax.config b/conf/pipeline/rnaseq/uppmax.config new file mode 100644 index 000000000..3e12a026c --- /dev/null +++ b/conf/pipeline/rnaseq/uppmax.config @@ -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.' + + // 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" + } + } +} diff --git a/conf/uppmax.config b/conf/uppmax.config index cbd0440ac..bb2b83332 100644 --- a/conf/uppmax.config +++ b/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 diff --git a/pipeline/rnaseq.config b/pipeline/rnaseq.config index 5b498344a..7ae199bd5 100644 --- a/pipeline/rnaseq.config +++ b/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" }