common-workflow-language

CWL documents describe workflows made of command line data analysis tools in a portable, reproducible, and reusable fashion.

Expected Behavior

cwltool --validate https://github.com/common-workflow-language/cwl-v1.2/raw/main/tests/conflict-wf.cwl validates all objects inthe file.

Actual Behavior

Tell us what happens instead

INFO /usr/bin/cwltool 3.0.20200807132242
ERROR Tool definition failed initialization:
Tool file contains graph of multiple objects, must specify one of #echo, #cat, #collision

Can someone explain to me how to use InitialWorkDir requirements without any input parameters.
For instance, I need to put my shell scripts near with cwl script and run them from that cwl script. Is there some way don't use absolute path to scripts? I tried to use EnvVariable like that:

baseCommand: sh
arguments: [$SCRIPT_FOLDER/script.sh]

But it is not working.

Then I foun

common-workflow-language

Here are 56 public repositories matching this topic...

common-workflow-language / common-workflow-language

DataBiosphere / toil

broadinstitute / cromwell

common-workflow-language / cwltool

Expected Behavior

Actual Behavior

rabix / composer

Barski-lab / cwl-airflow

rabix / bunny

sbg / sevenbridges-python

rabix / cwl-ts

rabix / benten

sbg / sevenbridges-r

common-workflow-language / cwlviewer

PMCC-BioinformaticsCore / janis

otiai10 / cwl.go

CompEpigen / CWLab

otiai10 / yacle

giannisdoukas / ipython2cwl

common-workflow-language / cwl-utils

common-workflow-language / user_guide

sbg / sevenbridges-cwl

crim-ca / weaver

common-workflow-language / cwltest

suecharo / genpei

tom-tan / cwl-inspector

tom-tan / ep3

EBI-Metagenomics / pipeline-v5

common-workflow-language / cwl-website

EBI-Metagenomics / workflow-is-cwl

rabix / cwl-format

sbg / tidycwl