Comments (2)
@jjkoehorst What is your cwltool version? Can you give me an example I can try out? (I wasn't able to create a reproducer)
from runcrate.
Using the following command and version of cwl
> cwltool --outdir OUT --provenance PROV quality/longread_no_kraken.yaml
INFO /Users/jasperk/mambaforge/bin/cwltool 3.1.20230513155734
INFO [cwltool] /Users/jasperk/mambaforge/bin/cwltool --outdir OUT --provenance PROV quality/longread_no_kraken.yaml
INFO Resolved 'quality/longread_no_kraken.yaml' to 'file:///Volumes/Git/m-unlock/cwl/tests/quality/longread_no_kraken.yaml'
It looks that the workflow finishes nicely but in PROV only packed.cwl is present
}INFO Final process status is success
INFO [provenance] Finalizing Research Object
INFO [provenance] Research Object saved to /Volumes/Git/m-unlock/cwl/tests/PROV
(base) ➜ tests git:(dev) ✗ find PROV | grep cwl
PROV/snapshot/workflow_longread_quality.cwl
PROV/workflow/packed.cwl
PROV/metadata/provenance/workflow_20prepare_fasta_db.e8ff364c-ee48-4002-9405-d71de13defa0.cwlprov.xml
PROV/metadata/provenance/primary.cwlprov.jsonld
PROV/metadata/provenance/workflow_20prepare_fasta_db.e8ff364c-ee48-4002-9405-d71de13defa0.cwlprov.jsonld
PROV/metadata/provenance/workflow_20prepare_fasta_db.e8ff364c-ee48-4002-9405-d71de13defa0.cwlprov.provn
PROV/metadata/provenance/workflow_20prepare_fasta_db.e8ff364c-ee48-4002-9405-d71de13defa0.cwlprov.nt
PROV/metadata/provenance/workflow_20prepare_fasta_db.e8ff364c-ee48-4002-9405-d71de13defa0.cwlprov.ttl
PROV/metadata/provenance/primary.cwlprov.json
PROV/metadata/provenance/primary.cwlprov.xml
PROV/metadata/provenance/primary.cwlprov.nt
PROV/metadata/provenance/workflow_20prepare_fasta_db.e8ff364c-ee48-4002-9405-d71de13defa0.cwlprov.json
PROV/metadata/provenance/primary.cwlprov.ttl
PROV/metadata/provenance/primary.cwlprov.provn
The job file:
cat quality/longread_no_kraken.yaml
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
from runcrate.
Related Issues (20)
- Error from runcrate-analysis, scenario 2_a HOT 1
- Error from runcrate-analysis, scenario 4_a HOT 1
- CWLProv conversion: include creation datetime, size, checksum, format
- CWLProv conversion: add profile conformance HOT 1
- Handle distinct directories with same content
- Convert CWLProv to RO - TypeError: unhashable type: 'list'
- KeyError: <cwl_utils.parser.cwl_v1_2.CommandInputEnumSchema object at 0x10aa191e0> ?
- AttributeError: 'NoneType' object has no attribute 'rsplit' HOT 6
- Option to make data files more user friendly HOT 2
- Bag validation failed: data/.DS_Store exists on filesystem but is not in the manifest HOT 1
- schema_salad.exceptions.ValidationException tried... HOT 1
- KeyError: 'fastqc.cwl' while cwl file is in the provenance folder HOT 4
- Filenames not in ro-crate-metadata.json HOT 4
- AttributeError: 'CommandLineTool' object has no attribute 'rsplit' HOT 1
- Run: option to download remote inputs
- Error from runcrate convert HOT 2
- Data locations using manifest file HOT 1
- Basedir for data files HOT 1
- Support for ExpressionTool in convert HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from runcrate.