output definition JSON - Githubissues

biodavidjm commented 4 years ago

It is not entirely clear to me whether there is an automated way to generate this required file or must be created manually? Thanks!

leepc12 commented 4 years ago

Croo tries find this JSON file in a WDL script file (as a comment like #CROO out_def http://somewhere/your_pipeline.croo.json).

Ask developers of WDL to check if there is a Croo output definition JSON file for the WDL. ENCODE WDL pipelines all have it.

If it's for your own WDL file, then yes you need to create it manually.

byee4 commented 1 year ago

Hi,

Is there any documentation/ability to create an out definition.json file with optional outputs (ie. building a pipeline that handles stranded and unstranded data; if a user specifies stranded data, then I would expect nulls for unstranded output:

"unique_unstranded": {
      "path": "bam_to_signals/rep${i+1}/${basename}",
      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads",
      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Uniq .\\nsignal\"]",
      "subgraph": "cluster_rep${i+1}"
    }

)

Thank you!

ENCODE-DCC / croo

output definition JSON #14