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Description
Expected Behavior
We are using a when to check if a variable is given to a workflow or not to execute a specific step.
When this variable (a String[]) we apply a when: $(inputs.kraken_database !== null) check to see if this variable is given. In addition we apply a scatter on this variable to run it for each of the elements.
Actual Behavior
It tries to perform the scatter before the when is processed.
INFO [workflow ] starting step illumina_quality_kraken2
ERROR Unhandled exception
Traceback (most recent call last):
File "/usr/local/lib/python3.8/dist-packages/cwltool/workflow_job.py", line 731, in try_make_job
emptyscatter = [
File "/usr/local/lib/python3.8/dist-packages/cwltool/workflow_job.py", line 732, in <listcomp>
shortname(s) for s in scatter if len(cast(Sized, inputobj[s])) == 0
TypeError: object of type 'NoneType' has no len()
INFO [workflow ] completed permanentFail
Workflow Code
illumina_quality_kraken2:
label: Kraken2
doc: Taxonomic classification of FASTQ reads
when: $(inputs.kraken_database !== null)
run: ../kraken2/kraken2.cwl
scatter: database
in:
tmp_id: identifier
identifier:
valueFrom: $(inputs.tmp_id)_Qfiltered
threads: threads
kraken_database: kraken_database
database: kraken_database
forward_reads: phix_filter/out_forward_reads
reverse_reads: phix_filter/out_reverse_reads
paired_end:
default: true
out: [sample_report]
Your Environment
- cwltool version:
/usr/local/bin/cwltool 3.1.20220224085855
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