Change report extension to Rmd

quarto does funny things with the striping in grouped tables, and
you can't turn it off - the striping is automatically added. See
GitHub issue:
quarto-dev/quarto-cli#6945

README.md

@@ -19,7 +19,7 @@ python3 map_pmids.py --pmid-file test_input.csv --outfile test_output.tsv
 Once you have the mapping output file, you can generate a report about the matches.
 
 ```
-quarto render mapping_report.qmd -P mapping_results_file:test_output.tsv
+quarto render mapping_report.Rmd -P mapping_results_file:test_output.tsv
 ```
 
 A [WDL workflow](https://dockstore.org/workflows/github.com/UW-GAC/anvil-util-workflows/backup_data_tables:main?tab=info) is also provided on Dockstore and as a .WDL file.

map_pubmed_ids_to_pgs_catalog.wdl

@@ -63,8 +63,8 @@ task run_pubs_report {
         File publication_records_file
     }
     command <<<
-        cp /usr/local/primed-pgs-queries/query_pgs_by_pmids.qmd ./
-        R -e "rmarkdown::render('query_pgs_by_pmids.qmd', params=list(score_records_file='~{score_records_file}', metrics_records_file='~{metrics_records_file}', publication_records_file='~{publication_records_file}'))"
+        cp /usr/local/primed-pgs-queries/query_pgs_by_pmids.Rmd ./
+        R -e "rmarkdown::render('query_pgs_by_pmids.Rmd', params=list(score_records_file='~{score_records_file}', metrics_records_file='~{metrics_records_file}', publication_records_file='~{publication_records_file}'))"
     >>>
     output {
         File report_file = "query_pgs_by_pmids.html"