Merge pull request #24 from eberdan/patch-1

Update params_qc_nf-core.R

inst/rmarkdown/templates/rnaseq/skeleton/QC/params_qc_nf-core.R

@@ -1,11 +1,12 @@
 # info params
 
 # This is the file used to run nf-core or compatible to that
-metadata_fn='https://raw.githubusercontent.com/bcbio/bcbioR-test-data/main/rnaseq/nf-core/coldata.csv'
+metadata_fn='/Path/to/metadata/meta.csv'
 # This file is inside star_salmon/ folder
-# remove URL below to point to local files
-se_object=url('https://raw.githubusercontent.com/bcbio/bcbioR-test-data/main/rnaseq/nf-core/salmon.merged.gene_counts.rds')
-# This folder is in the output directory inside multiqc folder
-multiqc_data_dir='https://raw.githubusercontent.com/bcbio/bcbioR-test-data/main/rnaseq/nf-core/multiqc-report-data/'
+se_object=('/path/to/nf-core/output/salmon/salmon.merged.gene_counts.rds')
+# This folder called "multiqc_report_data" is inside the output directory star_salmon inside multiqc folder
+multiqc_data_dir='/path/to/nf-core/output/star_salmon/multiqc_report_data'
 # This file is inside the genome folder in the output directory
-gtf_fn='https://raw.githubusercontent.com/bcbio/bcbioR-test-data/main/rnaseq/nf-core/genome.filtered.gtf.gz'
+gtf_fn='/path/to/nf-core/output/genome/hg38.filtered.gtf'
+# Put hg38, mm10, mm39, or other
+genome='hg38'