Merge pull request #112 from umccr/metadata_remove

Remove metadata tidiers and portaldb queries

.Rbuildignore

@@ -1,36 +1,30 @@
-## r
-^data-raw$
-^dracarys\.Rproj$
+^CODE_OF_CONDUCT\.md$
+^Dockerfile$
 ^LICENSE\.md$
-^docs$
-^_pkgdown\.yaml$
-^pkgdown$
 ^README\.Rmd$
+^TODO\.md$
+^\.DS_Store$
 ^\.Rproj\.user$
-^vignettes$
-
-## python
-^setup\.py$
-^setup\.cfg$
-^pyproject\.toml$
-^dracarys$
-
-## misc
-^\.github$
-^nogit$
-^conda$
-^Dockerfile$
 ^\.bumpversion\.cfg$
-^\.pre-commit-config\.yaml$
+^\.dockerignore$
 ^\.dvc$
 ^\.dvcignore$
-^\.dockerignore$
-^CODE_OF_CONDUCT\.md$
-^\.DS_Store$
-
-## inst html
+^\.github$
+^\.pre-commit-config\.yaml$
+^_pkgdown\.yaml$
+^conda$
+^data-raw$
+^docs$
+^dracarys$
+^dracarys\.Rproj$
+^nogit$
+^pkgdown$
+^pyproject\.toml$
+^setup\.cfg$
+^setup\.py$
+^vignettes$
 inst/rmd/umccr_portal/html
-inst/rmd/umccr_workflows/umccrise/html
-inst/rmd/umccr_workflows/bcl_convert/html
 inst/rmd/umccr_workflows/alignment_qc/html
+inst/rmd/umccr_workflows/bcl_convert/html
+inst/rmd/umccr_workflows/umccrise/html
 inst/sandbox

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2
+    rev: v0.4.1
     hooks:
     -   id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
@@ -13,11 +13,14 @@ repos:
           )$
     -   id: use-tidy-description
     -   id: readme-rmd-rendered
+    -   id: pkgdown
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.6.0
     hooks:
     -   id: check-added-large-files
         args: ['--maxkb=200']
+    -   id: file-contents-sorter
+        files: '^\.Rbuildignore$'
 -   repo: local
     hooks:
     -   id: forbid-to-commit

NAMESPACE

@@ -51,22 +51,8 @@ export(gds_files_list)
 export(gds_files_list_filter_relevant)
 export(gds_volumes_list)
 export(glims_excel_read)
-export(glims_portal_read)
 export(ica_token_validate)
 export(match_regex)
-export(meta_bcl_convert)
-export(meta_oncoanalyser_wgs)
-export(meta_oncoanalyser_wgts_existing_both)
-export(meta_oncoanalyser_wts)
-export(meta_rnasum)
-export(meta_sash)
-export(meta_star_alignment)
-export(meta_tso_ctdna_tumor_only)
-export(meta_umccrise)
-export(meta_wgs_alignment_qc)
-export(meta_wgs_tumor_normal)
-export(meta_wts_alignment_qc)
-export(meta_wts_tumor_only)
 export(multiqc_column_map_append)
 export(multiqc_date_fmt)
 export(multiqc_parse_bargraph_plot)
@@ -76,8 +62,6 @@ export(multiqc_parse_raw)
 export(multiqc_parse_xyline_plot)
 export(multiqc_parse_xyline_plot_contig_cvg)
 export(multiqc_tidy_json)
-export(portal_meta_read)
-export(portal_meta_read_athena)
 export(rdf2tab)
 export(read)
 export(s3_files_list_filter_relevant)