From 308756bbefeb7ee9cec22009d9689bb5a6f2da49 Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Thu, 3 Jul 2025 11:18:11 -0400 Subject: [PATCH 1/3] use repositories now --- DESCRIPTION | 2 +- NEWS.md | 4 ++++ R/helpers.R | 16 ++++++++++------ 3 files changed, 15 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d539bcf..efe7307 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: bcbioR Type: Package Title: Templates and functions to guide downstream analysis and data interpretation -Version: 0.4.4 +Version: 0.4.5 Authors@R: person("Pantano", "Lorena", , "lorena.pantano@gmail.com", role = c("aut", "cre")) Description: Collaborative code repository at the Harvard Chan Bioinformatics Core. diff --git a/NEWS.md b/NEWS.md index 83a2cfd..29f4c2e 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# bcbioR 0.4.5 + +Migrate templates to bcbio individual repositories + # bcbioR 0.4.4 init QC single cell adding init file for params for single QC #123 diff --git a/R/helpers.R b/R/helpers.R index d782f33..83266f5 100644 --- a/R/helpers.R +++ b/R/helpers.R @@ -83,9 +83,9 @@ bcbio_templates <- function(type="rnaseq", outpath=NULL, org=NULL){ #file.copy(fpath, outpath, recursive = T) copy_templates(outpath, "spatial", org) }, - chipseq={ + peakseq={ #file.copy(fpath, outpath, recursive = T) - copy_templates(outpath, "chipseq", org) + copy_templates(outpath, "peakseq", org) }, multiomics={ #file.copy(fpath, outpath, recursive = T) @@ -93,7 +93,7 @@ bcbio_templates <- function(type="rnaseq", outpath=NULL, org=NULL){ }, { stop(paste('project type not recognize, please choose: ', - 'rnaseq', 'chipseq', + 'rnaseq', 'peakseq', 'singlecell','singlecell_delux','spatial')) } ) @@ -220,10 +220,14 @@ copy_templates <- function(path, pipeline, org=NULL){ }else if(pipeline=="multiomics"){ parts = c("templates/multiomics") }else if(pipeline=="spatial"){ - parts = c("templates/spatial") + # parts = c("templates/spatial") + repos = "https://github.com/bcbio/spatial-reports/archive/refs/heads/main.zip" + names(repos)="spatial-reports" # apps=c(apps, SpatialViz="https://github.com/hbc/RShiny_app-SpatialViz/archive/refs/tags/Latest.zip") - }else if(pipeline=="chipseq"){ - parts = c("templates/chipseq") + }else if(pipeline=="peakseq"){ + # parts = c("templates/chipseq") #https://github.com/bcbio/peakseq-reports + repos = "https://github.com/bcbio/peakseq-reports/archive/refs/heads/main.zip" + names(repos)="peakseq-reports" } #check if it is url or folder From 5e130b29bc7714d80bc98e2ca82fab7451fb58aa Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Fri, 11 Jul 2025 16:19:59 -0400 Subject: [PATCH 2/3] add mm39 https://github.com/bcbio/rnaseq-reports/issues/48 --- inst/extdata/annotation/mm39.rna.gtf.gz | Bin 0 -> 21818 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 inst/extdata/annotation/mm39.rna.gtf.gz diff --git a/inst/extdata/annotation/mm39.rna.gtf.gz 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changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index 29f4c2e..5c3e941 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,7 @@ # bcbioR 0.4.5 Migrate templates to bcbio individual repositories +Add mm39 rRNA and tRNA annotation # bcbioR 0.4.4