Add more nf tests #655
Open
Add more nf tests #655
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
|
|
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. |
|
Should we also add |
LilyAnderssonLee
requested review from
LilyAnderssonLee and
jfy133
as code owners
Yes! On my to-do list, just started with the test config first :) |
|
So will you add all those nf-test to this PR? |
|
I was thinking one PR for each config. |
added 9 commits
October 24, 2025 10:06
jfy133
reviewed
Oct 29, 2025
There was a problem hiding this comment.
We are getting pretty close now!
- Minor: check indentation of the lines so they are consistent
- Minor: in a few places you have put the stable_name, stable_contents in a list, but not others, I don't know why you've done this but I don't think it's necessary(?) and if yes I would try and be consistent across all
- You don't need to separate snapshots per direct and assertion type, you can include multiple assertion types in a single named snapshot (I wrote a couple of examples as suggestions
- It appears when you are checking specific files you are only calling single samples, I would apply the same assertion across all samples of a file
- You explicitly call
.md5to generate these, you shouldn't need to do this - just give thepath()(using the.md5function removes the file name, so it's harder to know which md5sum corresponds to which file in the snapshot
|
|
||
| { assert snapshot ( stable_name_all ).match("all_files") }, | ||
| { assert snapshot ( stable_name_multiqc ).match("multiqc" ) }, | ||
| { assert snapshot( file("$outputDir/bbduk/2613_ERR5766181.bbduk.log").text.contains("Reads Processed:"), [stable_content_bbduk, stable_name_bbduk]).match("bbduk")}, |
There was a problem hiding this comment.
Why have you put content/name as a list here?, they can be independent entries
| { assert snapshot(path("$outputDir/metaphlan/metaphlan4/2613_metaphlan4.metaphlan_profile.txt").md5).match("metaphlan_profile_md5") }, | ||
| { assert snapshot ( stable_name_nanoq, file ("$outputDir/nanoq/ERR3201952_ERR3201952_filtered.stats").text.contains("Median read quality")).match("nanoq") }, | ||
| { assert snapshot(path("$outputDir/nanoq/ERR3201952_ERR3201952_filtered.stats").md5).match("nanoq_md5") }, | ||
| { assert snapshot ( file ("$outputDir/porechop_abi/ERR3201952_ERR3201952_porechop_abi.log").text.contains("reads were split"), [stable_name_porechopabi, stable_content_porechopabi]).match("porechop_abi") }, |
| { assert snapshot ( file ("$outputDir/fastp/2613_ERR5766181.fastp.log").text.contains("Read pairs merged"),[stable_content_fastp, stable_name_fastp] ).match("fastp") }, | ||
| { assert snapshot ( stable_name_ganon, file ("$outputDir/ganon/db1/2613_db1.ganon.tre").text.contains("Saccharomycetales")).match("ganon") }, | ||
| { assert snapshot(path("$outputDir/ganon/db1/2613_db1.ganon.tre").md5).match("ganon_md5") }, | ||
| { assert snapshot ( file ("$outputDir/kaiju/db6/2614_db6.kaiju.tsv").text.contains("ERR3201952.3225565"),[stable_content_kaiju, stable_name_kaiju] ).match("kaiju") }, |
| { assert snapshot(path("$outputDir/centrifuge/db3/2613_db3.centrifuge.report.txt").md5).match("centrifuge_md5") }, | ||
| { assert snapshot ( file ("$outputDir/fastp/2613_ERR5766181.fastp.log").text.contains("Read pairs merged"),[stable_content_fastp, stable_name_fastp] ).match("fastp") }, | ||
| { assert snapshot ( stable_name_ganon, file ("$outputDir/ganon/db1/2613_db1.ganon.tre").text.contains("Saccharomycetales")).match("ganon") }, | ||
| { assert snapshot(path("$outputDir/ganon/db1/2613_db1.ganon.tre").md5).match("ganon_md5") }, |
There was a problem hiding this comment.
Why are you only checking a single sample here? And same for the others...
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
This is a draft of adding nf-tests.
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).