Hi Firecloud team,
Is this a regression, a bug, or not intended functionality:
I am trying to run a workflow, but I don't want to write all outputs to annotations because it clutters the workspace.
Previously, I left the fields blank (I want the files in the workspace bucket, but not in annotations)
Now it looks like when I run this workflow the data model is not updated at all. Here's an example:
I expect the bottom two annotations to be written, but it looks like they are not.
Image may be NSFW.
Clik here to view.
Nothing too strange in the output WDL as far as I can tell
output {
File gatk_cnv_coverage_file = "${entity_id}.coverage.tsv"
File gatk_cnv_seg_file = "${entity_id}.seg"
File gatk_cnv_tn_coverage = "${entity_id}.tn.tsv"
File gatk_cnv_pre_tn_coverage = "${entity_id}.preTN.tsv"
File gatk_het_ad_normal = "${entity_id}.normal.hets.tsv"
File gatk_het_ad_tumor = "${entity_id}.tumor.hets.tsv"
Array[File] gatk_cnv_all_plots = glob("plotting/*.png")
File gatk_acnv_plot = "plotting_acnv/${entity_id}_ACNV.png"
File gatk_acnv_seg_file = "acnv/${entity_id}-sim-final.acs.seg"
}