air format (GitHub Actions)

Author: github-actions[bot]

code/main.R

@@ -12,38 +12,93 @@ setup_capsule_environment()
 # parse CLI arguments
 parser <- ArgumentParser()
 
-parser$add_argument("--count_type", type="character", default="clean")
-parser$add_argument("--feature_id_colname", type="character", default=NULL, help="Column name for feature IDs")
-parser$add_argument("--sample_id_colname", type="character", default=NULL, help="Column name for sample IDs")
-parser$add_argument("--group_colname", type="character", default="Group", help="Column name for sample groups")
-parser$add_argument("--label_colname", type="character", default=NULL, help="Column name for sample labels")
-parser$add_argument("--minimum_count_value_to_be_considered_nonzero", type="integer", default=8, help="Minimum count threshold")
-parser$add_argument("--minimum_number_of_samples_with_nonzero_counts_in_total", type="integer", default=7, help="Minimum samples with nonzero counts")
-parser$add_argument("--minimum_number_of_samples_with_nonzero_counts_in_a_group", type="integer", default=3, help="Minimum samples per group with nonzero counts")
-parser$add_argument("--use_cpm_counts_to_filter", type="logical", default=TRUE, help="Transform to CPM before filtering")
-parser$add_argument("--use_group_based_filtering", type="logical", default=FALSE, help="Use group-based filtering")
-parser$add_argument("--plot_corr_matrix_heatmap", type="logical", default=TRUE, help="Plot correlation heatmap")
-parser$add_argument("--interactive_plots", type="logical", default=FALSE, help="Create interactive plots with plotly")
+parser$add_argument("--count_type", type = "character", default = "clean")
+parser$add_argument(
+  "--feature_id_colname",
+  type = "character",
+  default = NULL,
+  help = "Column name for feature IDs"
+)
+parser$add_argument(
+  "--sample_id_colname",
+  type = "character",
+  default = NULL,
+  help = "Column name for sample IDs"
+)
+parser$add_argument(
+  "--group_colname",
+  type = "character",
+  default = "Group",
+  help = "Column name for sample groups"
+)
+parser$add_argument(
+  "--label_colname",
+  type = "character",
+  default = NULL,
+  help = "Column name for sample labels"
+)
+parser$add_argument(
+  "--minimum_count_value_to_be_considered_nonzero",
+  type = "integer",
+  default = 8,
+  help = "Minimum count threshold"
+)
+parser$add_argument(
+  "--minimum_number_of_samples_with_nonzero_counts_in_total",
+  type = "integer",
+  default = 7,
+  help = "Minimum samples with nonzero counts"
+)
+parser$add_argument(
+  "--minimum_number_of_samples_with_nonzero_counts_in_a_group",
+  type = "integer",
+  default = 3,
+  help = "Minimum samples per group with nonzero counts"
+)
+parser$add_argument(
+  "--use_cpm_counts_to_filter",
+  type = "logical",
+  default = TRUE,
+  help = "Transform to CPM before filtering"
+)
+parser$add_argument(
+  "--use_group_based_filtering",
+  type = "logical",
+  default = FALSE,
+  help = "Use group-based filtering"
+)
+parser$add_argument(
+  "--plot_corr_matrix_heatmap",
+  type = "logical",
+  default = TRUE,
+  help = "Plot correlation heatmap"
+)
+parser$add_argument(
+  "--interactive_plots",
+  type = "logical",
+  default = FALSE,
+  help = "Create interactive plots with plotly"
+)
 
 args <- parser$parse_args()
 
 # load multiOmicDataSet from data directory
 moo <- load_moo_from_data_dir()
 
 # run MOSuite
-moo |> 
-    filter_counts(
-        count_type = args$count_type,
-        feature_id_colname = args$feature_id_colname,
-        sample_id_colname = args$sample_id_colname,
-        group_colname = args$group_colname,
-        label_colname = args$label_colname,
-        minimum_count_value_to_be_considered_nonzero = args$minimum_count_value_to_be_considered_nonzero,
-        minimum_number_of_samples_with_nonzero_counts_in_total = args$minimum_number_of_samples_with_nonzero_counts_in_total,
-        minimum_number_of_samples_with_nonzero_counts_in_a_group = args$minimum_number_of_samples_with_nonzero_counts_in_a_group,
-        use_cpm_counts_to_filter = args$use_cpm_counts_to_filter,
-        use_group_based_filtering = args$use_group_based_filtering,
-        plot_corr_matrix_heatmap = args$plot_corr_matrix_heatmap,
-        interactive_plots = args$interactive_plots
-        ) |> 
-    write_rds(file.path(getOption("moo_plots_dir"), "..", "moo", "moo-filt.rds"))
+moo |>
+  filter_counts(
+    count_type = args$count_type,
+    feature_id_colname = args$feature_id_colname,
+    sample_id_colname = args$sample_id_colname,
+    group_colname = args$group_colname,
+    label_colname = args$label_colname,
+    minimum_count_value_to_be_considered_nonzero = args$minimum_count_value_to_be_considered_nonzero,
+    minimum_number_of_samples_with_nonzero_counts_in_total = args$minimum_number_of_samples_with_nonzero_counts_in_total,
+    minimum_number_of_samples_with_nonzero_counts_in_a_group = args$minimum_number_of_samples_with_nonzero_counts_in_a_group,
+    use_cpm_counts_to_filter = args$use_cpm_counts_to_filter,
+    use_group_based_filtering = args$use_group_based_filtering,
+    plot_corr_matrix_heatmap = args$plot_corr_matrix_heatmap,
+    interactive_plots = args$interactive_plots
+  ) |>
+  write_rds(file.path(getOption("moo_plots_dir"), "..", "moo", "moo-filt.rds"))