diff --git a/inst/rmarkdown/templates/rnaseq/skeleton/params_de.R b/inst/rmarkdown/templates/rnaseq/skeleton/params_de.R index c55baed..a04b1b3 100644 --- a/inst/rmarkdown/templates/rnaseq/skeleton/params_de.R +++ b/inst/rmarkdown/templates/rnaseq/skeleton/params_de.R @@ -10,6 +10,6 @@ root = "../.." date = "YYYYMMDD" column = "sample_type" subset_column = NA -metadata_fn = "/n/data1/cores/bcbio/platform/bcbioR-test-data/rnaseq/bcbio/coldata.csv" -counts_fn = '/n/data1/cores/bcbio/platform/bcbioR-test-data/rnaseq/bcbio/tximport-counts.csv' +metadata_fn = "https://raw.githubusercontent.com/bcbio/bcbioR-test-data/main/rnaseq/bcbio/coldata.csv" +counts_fn = 'https://raw.githubusercontent.com/bcbio/bcbioR-test-data/main/rnaseq/bcbio/tximport-counts.csv' basedir <- 'results' diff --git a/inst/rmarkdown/templates/rnaseq/skeleton/params_qc.R b/inst/rmarkdown/templates/rnaseq/skeleton/params_qc.R index 894469a..505561d 100644 --- a/inst/rmarkdown/templates/rnaseq/skeleton/params_qc.R +++ b/inst/rmarkdown/templates/rnaseq/skeleton/params_qc.R @@ -6,5 +6,5 @@ aim = 'short description' analyst = 'person in the core' -metadata_fn="/n/data1/cores/bcbio/platform/bcbioR-test-data/rnaseq/bcbio/coldata.csv" -se_object="/n/data1/cores/bcbio/platform/bcbioR-test-data/rnaseq/bcbio/bcbio-se.rds" +metadata_fn='https://raw.githubusercontent.com/bcbio/bcbioR-test-data/main/rnaseq/bcbio/coldata.csv' +se_object=url("https://raw.githubusercontent.com/bcbio/bcbioR-test-data/main/rnaseq/bcbio/bcbio-se.rds")