Refer to the CWL CommandLineTool Specification for further explanation about many of the properties described below. Not all features described in the specification are supported.
$(inputs.InputFASTA)
{type: array, items: [File, Directory]}
scatter
and scatterMethod
fields.--output-filename
$(inputs.inputSAM.nameroot).bam
/tmp/storage/SRR45678_sorted.sam
SRR45678_sorted.bam
❗️ Modifying data within the CWL editor can result in invalid code.
python /path/to/script.py
such that python
and /path/to/script.py
are added in separate lines.Entry name
(e.g. runner.sh
) and the script content under Entry
. Then, point your base command to that custom script, e.g. bash runner.sh
.❗️ What's the difference between Settings and Arguments?Settings are exposed at the pipeline level with the ability to get modified at launch, while Arguments are intended to be immutable and hidden from users launching the pipeline.
$(inputs.InputSetting)
$(inputs.InputFile.path)
. For additional information please refer to the File CWL documentation.bash script.sh $1 $2