galaxyproject / galaxyproject/planemo
planemo lint workflow tests improvement
- Dominant language
- Python
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- Avg merge
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Description
This test:
```yml
- doc: Test outline for scrna-seq-fastq-to-matrix-10X-cellplex.ga
job:
fastq PE collection GEX:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: subsample
elements:
- identifier: forward
class: File
location: https://zenodo.org/records/10229382/files/subSample_GEX_R1.fastq.gz
filetype: fastqsanger.gz
- identifier: reverse
class: File
location: https://zenodo.org/records/10229382/files/subSample_GEX_R2.fastq.gz
filetype: fastqsanger.gz
...
outputs:
CITE-seq-Count report:
class: Collection
collection_type: list
elements:
identifier: subsample
class: File
asserts:
- that: "has_line"
line: "CITE-seq-Count Version: 1.4.4"
- that: "has_line"
line: "Reads processed: 1171367"
...
```
Passes the workflow_lint but the test will fail with the following error message:
`No path specified for expected output file [CITE-seq-Count report]`
The correct grammar is:
```
...
CITE-seq-Count report:
class: Collection
collection_type: list
element_tests:
subsample:
asserts:
- that: "has_line"
line: "CITE-seq-Count Version: 1.4.4"
- that: "has_line"
line: "Reads processed: 1171367"
...
```
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