inputBinding and use $(inputs.sqlStatement) (instead of $4); or keep the inputBinding and drop the $4
Cool.
I am using:
arguments: [ -c, sevenbridges, -q, $(inputs.sqlStatement) ]
inputs:
sqlStatement:
type: string
I kept the $(inputs.sqlStatement), just looks cleaner. ;)
Thank you very much.
I am getting additional info that is causing some problem with my logs.
I would like to eliminate the following in parameters:
--mount=type=bind,source=/private/tmp/docker_tmpioxvy1rg,target=/WXCNAB \
--mount=type=bind,source=/private/tmp/docker_tmpimf66_tj,target=/tmp \
--workdir=/WXCNAB \
--read-only=true \
--user=501:20 \Same with --user, --workdir, ...
I have only:
cwlVersion: v1.2
class: CommandLineTool
requirements:
DockerRequirement:
dockerPull: sbg-snowflake
NetworkAccess:
networkAccess: true
baseCommand: []
arguments: [ -c, sevenbridges, -o, log_level=DEBUG, -q, $(inputs.sqlStatement) ]
inputs:
sqlStatement:
type: string
https://www.commonwl.org/v1.2/CommandLineTool.html#Runtime_environment
All versions of CWL
Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility concerns of the implicit hidden execution point (For further discussion, see https://doi.org/10.12688/f1000research.15140.1).
https://www.commonwl.org/v1.2/CommandLineTool.html#DockerRequirement
Thank you I will read the docs and see.
I will see if the CommandLine Tool would be better after all.
INFO [job sqlsect] /private/tmp/docker_tmpxls1zfbd$ docker \
run \
-it \
--rm \
sbg-snowflake \
-c \
sevenbridges \
-q \
'SELECT 1 AS seq, CURRENT_VERSION() as version, CURRENT_TIMESTAMP() as timestamp;'
the input device is not a TTY
cwlVersion: v1.2
class: CommandLineTool
baseCommand: docker
arguments: [run, -i, --rm, sbg-snowflake, -c, sevenbridges, -q, $(inputs.sqlStatement)]
inputs:
sqlStatement:
type: string
outputs: []
common-workflow-language project, nor submit branches to the cwl-1.2.1 repository anymore (did both this week, pushed a branch to 1.2.1 last night).
1 reply
kinow@ranma:~/Development/java/workspace/cwlviewer$ git push -u upstream update-dependencies
ERROR: Permission to common-workflow-language/cwlviewer.git denied to kinow.
...Agenda & notes: https://w3id.org/cwl/meeting_minutes
Direct link to video room: https://matrix.to/#/#cwl_conf:matrix.org
I tried : when: $(inputs.in2 !== null)
and different variations but cannot seem to get the right result
Agenda & notes: https://w3id.org/cwl/meeting_minutes
Direct link to video room: https://matrix.to/#/#cwl_conf:matrix.org
that looks good - but, can I take files that pre-exist in a docker container, rather than passing them into the workflow as an input, and use them in my workflow?
This is the expression tool I'm working on: https://github.com/UoMResearchIT/wrf_emep_cwl_workflow/blob/master/cwl/create_run_dir.cwl - the directory I'm interested in is /usr/local/WRF/run, which is included with the software as a template running directory
CommandLineTool that copies the files you want into the current working directory (. or $(runtime.outdir)); then glob them up like any other outputs