Template to Component

R/nextflow_annotation_utils.R

@@ -333,9 +333,11 @@ annotate_aligned_reads <- function(metadata,
                                    verbose = TRUE) {
 
   outputFrom <- attr(metadata, "outputFrom")
+  template <- sub("bts:", "", attr(metadata, "template"))
   if(verbose) message("Running annotate_aligned_reads for ", outputFrom)
 
   format_as <- annotation_rule(outputFrom, "format_as")
+  metadata[, Component := template]
   metadata[, fileFormat := format_as(Filename)]
   metadata[, dataType := "AlignedReads"]
   metadata[, dataSubtype := "processed"]
@@ -369,13 +371,15 @@ annotate_quantified_expression <- function(metadata,
                                            verbose = TRUE) {
 
   outputFrom <- attr(metadata, "outputFrom")
+  template <- sub("bts:", "", attr(metadata, "template"))
   if(verbose) message("Running annotate_quantified_expression for ", outputFrom)
 
   format_as <- annotation_rule(outputFrom, "format_as")
   expression_unit <- switch(outputFrom,
                             "STAR and Salmon" = "TPM",
                             "featureCounts" = "Counts")
 
+  metadata[, Component := template]
   metadata[, fileFormat := format_as(Filename)]
   metadata[, dataType := "geneExpression"]
   metadata[, dataSubtype := "processed"]
@@ -402,6 +406,7 @@ annotate_called_variants <- function(metadata,
                                      verbose = TRUE) {
 
     outputFrom <- attr(metadata, "outputFrom")
+    template <- sub("bts:", "", attr(metadata, "template"))
     if(verbose) message("Running annotate_called_variants for ",  outputFrom)
 
     # vcfs can be annotated type, workflow stops at Variant Calling bc we run a custom nf-vcf2maf
@@ -422,6 +427,7 @@ annotate_called_variants <- function(metadata,
     }
 
     format_as <- annotation_rule(outputFrom, "format_as")
+    metadata[, Component := template]
     metadata[, fileFormat := format_as(Filename)]
     metadata[, dataType := data_type_assign(Filename, fileFormat), by = entityId]
     metadata[, dataSubtype := "processed"]

R/provenance.R

@@ -1,18 +1,18 @@
 #' Add activity to entity
-#' 
+#'
 #' Util for adding activity info to a file entity.
 #' See also https://help.synapse.org/docs/Provenance.1972470373.html
-#' 
+#'
 #' @param entity Synapse entity id.
 #' @param act_name Name of activity.
 #' @param act_executed Reference to the the activity executed (URL preferred).
 #' @param used_inputs Vector of inputs for this act, e.g. syn ids, links to other data sources, etc.
 #' @export
-add_activity <- function(entity, 
+add_activity <- function(entity,
                          act_name,
                          act_executed,
                          used_inputs) {
- 
+
     act <- synapseclient$Activity(name = act_name,
                                   executed = act_executed,
                                   used = used_inputs)
@@ -21,22 +21,22 @@ add_activity <- function(entity,
 }
 
 #' Add activity to multiple entities
-#' 
-#' Wrapper provenance function that does a little more work to 
+#'
+#' Wrapper provenance function that does a little more work to
 #' expand many-to-many mappings to create records of entity, activity, and input.
-#' 
-#' @param entities Vector or list of entities. 
+#'
+#' @param entities Vector or list of entities.
 #' @param act_name Vector or list of activity name.
 #' @param act_executed Vector or list of reference activity executed.
 #' @param used_inputs Vector or list of inputs for each entity.
 #' @import data.table
 #' @export
-add_activity_batch <- function(entities, 
+add_activity_batch <- function(entities,
                                act_name,
                                act_executed,
                                used_inputs
                              ) {
-  
+
   stopifnot(lengths(list(entities, act_name, act_executed, used_inputs)) > 0)
   if(is.list(entities)) {
     if(length(used_inputs) > 1) used_inputs <- rep(used_inputs, lengths(entities))
@@ -56,4 +56,18 @@ delete_provenance <- function(entities) {
   for(i in entities) {
     .syn$deleteProvenance(entity)
   }
-}
+}
+
+### Validate manifest
+
+Manifests can be inspected and validated using schematic before submission.
+To do so, it has to be written to a .csv first.
+
+```{r rnaseq-meta-validate, eval=FALSE}
+
+manifest_1 <- meta$manifests$`STAR and Salmon`
+template <- sub("bts:", "", attr(manifest_1, "template"))
+fwrite(manifest_1, "manifest_1.csv")
+manifest_validate(data_type = template, file_name = "manifest_1.csv")
+
+```