Better content tests #416
Merged
Better content tests #416
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Member
|
Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.3.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
tests/default.nf.test
Outdated
| { assert path("${params.outdir}/samtools/megahit.SAMPLE1_PE.idxstats").readLines().size() > 1600 }, | ||
| { assert path("${params.outdir}/prodigal/megahit.prodigal.gff.gz").linesGzip.findAll { l -> l.contains('CDS') }.size() > 3000 }, | ||
| { assert path("${params.outdir}/summary_tables/megahit.prodigal.counts.tsv.gz").linesGzip.size() > 3000 }, | ||
| { assert path("${params.outdir}/summary_tables/megahit.prodigal.counts.tsv.gz").linesGzip.size() > 3000 }, |
There was a problem hiding this comment.
this is a duplicate of the line no46
mariaTsontaki
approved these changes
Oct 29, 2025
tests/default.nf.test
Outdated
| { assert path("${params.outdir}/samtools/megahit.SAMPLE1_PE.idxstats").readLines().size() > 1600 }, | ||
| { assert path("${params.outdir}/prodigal/megahit.prodigal.gff.gz").linesGzip.findAll { l -> l.contains('CDS') }.size() > 3000 }, | ||
| { assert path("${params.outdir}/summary_tables/megahit.prodigal.counts.tsv.gz").linesGzip.size() > 3000 }, | ||
| { assert path("${params.outdir}/summary_tables/megahit.prodigal.counts.tsv.gz").linesGzip.size() > 3000 }, |
There was a problem hiding this comment.
Suggested change
| { assert path("${params.outdir}/summary_tables/megahit.prodigal.counts.tsv.gz").linesGzip.size() > 3000 }, |
There was a problem hiding this comment.
looks good @erikrikarddaniel!
the only thing pending would be to re-run the nf-test for the snapshots to be updated, after the test is corrected.
There was a problem hiding this comment.
my bad: the output of this assert is not included in the snapshot, so no need to rerun the test
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).This adds more content tests to the default test: summing columns in overall_stats and counts.