From 21dd35b71de8a5eb1aeddd2f12fc4f1ba76cb57f Mon Sep 17 00:00:00 2001 From: Andrey Kislyuk Date: Fri, 5 Mar 2021 15:56:05 -0800 Subject: [PATCH] Fix typo in miniwdl check FAQ; normalize style --- docs/FAQ.md | 44 +++++++++++++++++++++----------------------- 1 file changed, 21 insertions(+), 23 deletions(-) diff --git a/docs/FAQ.md b/docs/FAQ.md index c09c6948..d80a0b88 100644 --- a/docs/FAQ.md +++ b/docs/FAQ.md @@ -14,64 +14,62 @@ Also there is an embedded short course 'learn-miniwdl' which includes screencast ### Install and verify miniwdl - Q: miniwdl won't intall (or work) on my machine - - verify installation of Python 3.6+ - - verify installation of Docker + - Verify installation of Python 3.6+ + - Verify installation of Docker. - Q: miniwdl isn't working on my Mac - - verify Docker version (17+) and user permission for Docker - - you'll first need to override the `TMPDIR` environment variable, e.g. `export TMPDIR=/tmp` - - to allow Docker containers to mount shared working directories. + - Verify Docker version (17+) and user permission for Docker. + - You'll first need to override the `TMPDIR` environment variable, e.g. `export TMPDIR=/tmp` to allow Docker containers to mount shared working directories. - Please [file any other issues](https://github.com/chanzuckerberg/miniwdl/issues) that arise! - Q: the ```miniwdl run``` command won't run my WDL workflow - - verify that each workflow task runs from a Docker container image - - define the container image in the WDL script (task section(s)) + - Verify that each workflow task runs from a Docker container image. + - Define the container image in the WDL script (task section(s)). -- Q: what is the quickest way to verify that miniwdl is properly installed - - run ```miniwdl --help``` and review the list of possible commands +- Q: what is the quickest way to verify that miniwdl is properly installed? + - Run ```miniwdl --help``` and review the list of possible commands. --- ### Run WDL workflow with the ```miniwdl run``` command - Q: what is simplest way to test running a WDL workflow on miniwdl? - - run ```miniwdl run_self_test``` - it includes an example workflow - - verify this job returns the ```ok``` and ```done``` messages as expected + - Run ```miniwdl run_self_test``` - it includes an example workflow. + - Verify this job returns the ```ok``` and ```done``` messages as expected. - Q: how can I run a quick ```hello.wdl``` WDL workflow? - - copy [this file](https://github.com/openwdl/learn-wdl/blob/master/6_miniwdl_course/1_hello.wdl) to your miniwdl dev env - - run ```miniwdl run hello.wdl```, there are no input parameters used in this quick test + - Copy [this file](https://github.com/openwdl/learn-wdl/blob/master/6_miniwdl_course/1_hello.wdl) to your miniwdl development environment. + - Run ```miniwdl run hello.wdl```, there are no input parameters used in this quick test. - Q: Where is the job output from miniwdl job? - miniwdl produces workflow, task and job logs as well as task output. - - See the folder\file structure generated for each job run for these files. + - See the folder\file structure generated for each job run for these files. - Q: What does ```miniwdl run myfile.wdl``` do? - - If your WDL file defines inputs and outputs - - then it prints a list of inputs and outputs and notes which inputs are required + - If your WDL file defines inputs and outputs, then it prints a list of inputs and outputs and notes which inputs are required. - Q: How to do I assign values to input variables when I use miniwdl to run a WDL file? - you can assign directly on the command line, i.e. ```miniwdl run myfile.wdl input1=input.bam input2= input.bai, etc...``` - or you can use the ```--input``` flag and assign input values via an ```input.json``` file - Q: How can I get more information about job execution? - - run the ```miniwdl run myfile.wdl``` command - - use the ```--verbose``` flag + - Run the ```miniwdl run myfile.wdl``` command + - Use the ```--verbose``` flag - Q: What is the ```_LAST``` directory? - - miniwdl generates a symbolic link `_LAST` pointing to the timestamped subdirectory for most recent run - - and an `out` directory tree containing symbolic links to the output files. + - miniwdl generates a symbolic link `_LAST` pointing to the timestamped subdirectory for most recent run, + and an `out` directory tree containing symbolic links to the output files. --- ### Check WDL syntax with the ```miniwdl check``` command - Q: When I run ```miniwdl check myfile.wdl``` it doesn't produce any output - - re-run the command, sometimes it takes a couple of seconds to complete the WDL file parsing + - Re-run the command, sometimes it takes a couple of seconds to complete the WDL file parsing - Q: Do I have to fix all of items listed (warnings) in the results of ```miniwdl check myfile.wdl``` - - this command generates both errors (which you optionally fix) and warnings (which you must fix). - - warnings are shown in red. + - This command generates both warnings (which you optionally fix) and errors (which you must fix). + - Warnings are shown in red. ---