galaxyproject / galaxyproject/planemo
Workflow testing reports number of tests incorrectly
- Dominant language
- Python
- Stars
- 110
- Forks
- 102
- Avg merge
- 4d 21h
- Merged PRs (30d)
- 13
Description
The following test.yml for the training material quality-control tutorial workflow provides a good illustration of the problem:
```
---
- doc: "Test sample data for Sequence-analyses:Quality-control"
job:
reads_1:
class: File
location: https://zenodo.org/record/61771/files/GSM461178_untreat_paired_subset_1.fastq
filetype: fastqsanger
reads_2:
class: File
location: https://zenodo.org/record/61771/files/GSM461178_untreat_paired_subset_2.fastq
filetype: fastqsanger
outputs:
reads_1_fastqc:
asserts:
has_text:
text: 'Sanger / Illumina 1.9'
reads_1_cutadapt:
asserts:
has_text:
text: '3,651,491 bp (98.7%)'
reads_2_fastqc:
asserts:
has_text:
text: 'Sequence length 37'
reads_cutadapt:
asserts:
has_text:
text: '98,624 (98.6%)'
multiqc:
asserts:
has_text:
text: 'FastQC'
```
This workflow test checks properties of 5 different output files, yet planemo reports:
`All 1 test(s) successfully executed.`
5 test(s) executed is what I would have expected.
Contributor guide
Research direction
Start with the test.yml workflow example in the issue and reproduce the report showing one test for five output files. Trace the workflow-test reporting entry point in planemo, then verify that the completed report counts the asserted output files individually and still reports successful execution.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, testing-qa
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100