Executing workflow from argument file with provenance not working as expected

[jjkoehorst]

Expected Behavior

When executing a workflow with the workflow in the argument yaml file using cwl:tool: works as expected.
When executing it with --provenance PROV the provenance should show all files and provenance elements.

Actual Behavior

However when executing it with --provenance PROV the provenance does not show any individual workflow files.

To explain it a bit in more detail...

When running the workflow using local cwl files it works

cwltool --outdir OUT --provenance PROV ../workflows/workflow_longread_quality.cwl longread_quality/no_kraken.yaml

find PROV | grep "cwl$"                                                                                          
PROV/snapshot/workflow_prepare_fasta_db.cwl
PROV/snapshot/minimap2_to_fastq.cwl
PROV/snapshot/filtlong.cwl
PROV/snapshot/pigz.cwl
PROV/snapshot/prepare_fasta_db.cwl
PROV/snapshot/array_to_file.cwl
PROV/snapshot/krona.cwl
PROV/snapshot/files_to_folder.cwl
PROV/snapshot/nanoplot.cwl
PROV/snapshot/workflow_longread_quality.cwl
PROV/snapshot/concatenate.cwl
PROV/snapshot/kraken2.cwl
PROV/workflow/packed.cwl

When running it like

cwltool --outdir OUT --provenance PROV https://gitlab.com/m-unlock/cwl/-/raw/master/workflows/workflow_longread_quality.cwl longread_quality/no_kraken.yaml

find PROV | grep "cwl$"
PROV/workflow/packed.cwl

it does not show the individual cwl files. Neither when executing it like

cwl:tool: ../../workflows/workflow_longread_quality.cwl
# cwl:tool: https://gitlab.com/m-unlock/cwl/-/raw/master/workflows/workflow_longread_quality.cwl
identifier: TEST
readtype: Nanopore
fastq_rich: true
threads: 6
memory: 4000
longreads:
   - class: File
     location: http://download.systemsbiology.nl/unlock/cwl/test_data/ont_guppy_reads.fq.gz
filter_references:
   - class: File
     location: http://download.systemsbiology.nl/unlock/cwl/test_data/human_small.fa.gz

find PROV | grep "cwl$"
PROV/snapshot/workflow_longread_quality.cwl
PROV/workflow/packed.cwl

Workflow Code

# cwl:tool: <Depending on the type of run>
identifier: TEST
readtype: Nanopore
fastq_rich: true
threads: 6
memory: 4000
longreads:
   - class: File
     location: http://download.systemsbiology.nl/unlock/cwl/test_data/ont_guppy_reads.fq.gz
filter_references:
   - class: File
     location: http://download.systemsbiology.nl/unlock/cwl/test_data/human_small.fa.gz

Your Environment

• cwltool version: 3.1.20230513155734