diff --git a/.github/workflows/add-issues-to-project.yml b/.github/workflows/add-issues-to-project.yml index ccb77d7..a2dd579 100644 --- a/.github/workflows/add-issues-to-project.yml +++ b/.github/workflows/add-issues-to-project.yml @@ -13,11 +13,10 @@ jobs: name: Add issue to project runs-on: ubuntu-latest steps: - - uses: actions/add-to-project@244f685bbc3b7adfa8466e08b698b5577571133e + - uses: actions/add-to-project@5afcf98fcd03f1c2f92c3c83f58ae24323cc57fd #v2.0.0 with: # You can target a project in a different organization or user account # to the issue. # For organization projects: https://github.com/orgs/ORG_NAME/projects/PROJECT_NUMBER - # For user projects: https://github.com/users/USER_NAME/projects/PROJECT_NUMBER project-url: https://github.com/orgs/childrens-bti/projects/1 github-token: ${{ secrets.ADD_TO_PROJECT_PAT }} diff --git a/scripts/select-clinVar-submissions.R b/scripts/select-clinVar-submissions.R index 49d740f..7066a36 100644 --- a/scripts/select-clinVar-submissions.R +++ b/scripts/select-clinVar-submissions.R @@ -59,10 +59,10 @@ conflict_res <- opt$conflict_res ## load variant summary file, which reports latest ClinVar consensus calls for each variant variant_summary_df <- vroom(input_variant_summary, - delim = "\t", - col_types = c(ReferenceAlleleVCF = "c", AlternateAlleleVCF = "c", PositionVCF = "i", VariationID = "n"), - show_col_types = FALSE - ) %>% + delim = "\t", + col_types = c(ReferenceAlleleVCF = "c", AlternateAlleleVCF = "c", PositionVCF = "i", VariationID = "n"), + show_col_types = FALSE +) %>% dplyr::rename( AlleleID = dplyr::any_of(c("AlleleID", "#AlleleID")) ) %>% @@ -84,7 +84,7 @@ variant_summary_df <- vroom(input_variant_summary, dplyr::filter(!ReviewStatus %in% c( "no assertion provided", "no assertion criteria provided", - "no classification for the individual variant", + "no classification for the individual variant", "no classification provided", "no classification for the single variant", "no classifications from unflagged records" @@ -102,10 +102,10 @@ while (grepl("^#", readLines(con, n = 1))) { # Load submission file while skipping number of lines determined above submission_summary_df <- vroom(input_submission_file, - skip = skip_lines, - delim = "\t", - show_col_types = F - ) %>% + skip = skip_lines, + delim = "\t", + show_col_types = F +) %>% dplyr::rename( VariationID = dplyr::any_of(c("VariationID", "#VariationID")) ) @@ -155,16 +155,16 @@ submission_summary_df <- submission_summary_df %>% ) %>% dplyr::filter( !ReviewStatus %in% c( - "no assertion provided", + "no assertion provided", "no assertion criteria provided", - "no classification provided", + "no classification provided", "flagged submission" ), ClinicalSignificance %in% c( - "Pathogenic", - "Likely pathogenic", - "Benign", - "Likely benign", + "Pathogenic", + "Likely pathogenic", + "Benign", + "Likely benign", "Uncertain significance" ), # Filter on contributing records if this column is present in supplied file @@ -180,7 +180,7 @@ submission_merged_df <- submission_summary_df %>% dplyr::rename("LastEvaluated" = DateLastEvaluated) %>% left_join(variant_summary_df, by = "VariationID", - multiple = "all", + multiple = "all", suffix = c("_sub", "_var"), relationship = "many-to-many" ) %>% @@ -202,11 +202,11 @@ variants_no_conflict_expert <- submission_merged_df %>% variants_no_conflicts <- submission_merged_df %>% dplyr::filter(!VariationID %in% variants_no_conflict_expert$VariationID) %>% dplyr::filter( - ClinicalSignificance_sub == ClinicalSignificance_var | - is.na(ClinicalSignificance_var) | - (grepl("Pathogenic|Likely pathogenic", ClinicalSignificance_sub) & grepl("Pathogenic|Likely pathogenic", ClinicalSignificance_var)) | - (grepl("Benign|Likely benign", ClinicalSignificance_sub) & grepl("Benign|Likely benign", ClinicalSignificance_var)) | - (grepl("Uncertain significance", ClinicalSignificance_sub) & grepl("Uncertain significance", ClinicalSignificance_var)) + ClinicalSignificance_sub == ClinicalSignificance_var | + is.na(ClinicalSignificance_var) | + (grepl("Pathogenic|Likely pathogenic", ClinicalSignificance_sub) & grepl("Pathogenic|Likely pathogenic", ClinicalSignificance_var)) | + (grepl("Benign|Likely benign", ClinicalSignificance_sub) & grepl("Benign|Likely benign", ClinicalSignificance_var)) | + (grepl("Uncertain significance", ClinicalSignificance_sub) & grepl("Uncertain significance", ClinicalSignificance_var)) ) %>% dplyr::arrange(desc(mdy(LastEvaluated))) %>% distinct(VariationID, .keep_all = T) %>%