Can you fix the formatting of docs generated from WDL in method configurations?

LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

Hello,

When creating a new method configuration, it is possible to automatically generate the documentation from the WDL. A great feature.... However, the formatting gets ruined. Sometimes important usage information is in the docs and it becomes easy to miss (speaking from experience).

The example below is from a featured workspace.

The WDL:

## Copyright Broad Institute, 2017
##
## This WDL workflow runs GATK4 Mutect 2 on a single tumor-normal pair or on a single tumor sample,
## and performs additional filtering and functional annotation tasks.
##
## NOTE: this wdl is an exact copy of mutect2.wdl in the gatk repo except for replacing File with String in GATK task inputs in order to
## avoid localizing files in cromwell and thereby allowing the GATK engine to access cloud-based files with NIO.  Once
## cromwell supports "smart" File variables that know when and when not to localize the two wdls should be merged.
##
## Main requirements/expectations :
## - One analysis-ready BAM file (and its index) for each sample
##
## Description of inputs:
##
## ** Runtime ** 
## gatk_docker, oncotator_docker: docker images to use for GATK 4 Mutect2 and for Oncotator
## preemptible_attempts: how many preemptions to tolerate before switching to a non-preemptible machine (on Google)
## max_retries: how many times to retry failed tasks -- very important on the cloud when there are transient errors
## gatk_override: (optional) local file or Google bucket path to a GATK 4 java jar file to be used instead of the GATK 4 jar
##                in the docker image.  This must be supplied when running in an environment that does not support docker
##                (e.g. SGE cluster on a Broad on-prem VM)
##
......

The documentation that results:

Documentation:
Copyright Broad Institute, 2017 This WDL workflow runs GATK4 Mutect 2 on a single tumor-normal pair or on a single tumor sample, and performs additional filtering and functional annotation tasks. NOTE: this wdl is an exact copy of mutect2.wdl in the gatk repo except for replacing File with String in GATK task inputs in order to avoid localizing files in cromwell and thereby allowing the GATK engine to access cloud-based files with NIO. Once cromwell supports "smart" File variables that know when and when not to localize the two wdls should be merged. Main requirements/expectations : - One analysis-ready BAM file (and its index) for each sample Description of inputs: ** Runtime ** gatk_docker, oncotator_docker: docker images to use for GATK 4 Mutect2 and for Oncotator preemptible_attempts: how many preemptions to tolerate before switching to a non-preemptible machine (on Google) gatk_override: (optional) local file or Google bucket path to a GATK 4 java jar file to be used instead of the GATK 4 jar in the docker image. This must be supplied when running in an environment that does not support docker (e.g. SGE cluster on a Broad on-prem VM)

Many thanks,
Lee

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Hi Lee,

    Thank you for this suggestion. I'm moving it to our feature requests category so it can be seen and prioritized by our FireCloud product owners.

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