Snapshot for -profile test_single_end
#908
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dialvarezs
changed the title
-profile test_single_end
dialvarezs
requested review from
d4straub,
jfy133,
muabnezor and
prototaxites
as code owners
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jfy133
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Overall LGTM,
As a general thing, I suggest wrapping all asserts in snapshot even if it's just a boolean (you can also store these in a string even for more human readability, see nf-core/createtaxdb as an example -inspired by @maxulysse )
If that particular check fails and is not in a snapshot, it can be really annoying to debug.
I have 3 minor things that may have been missed, but otherwise this is looking very comprehensive, great work @dialvarezs !
| @@ -1,6 +1,12 @@ | |||
| .DS_Store | |||
| Ancient_DNA/pydamage/analyze/*/*.csv | |||
| Ancient_DNA/variant_calling/*/*.vcf.gz | |||
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No string check for these? Or you could use https://github.com/seppinho/nft-vcf
| .DS_Store | ||
| Ancient_DNA/pydamage/analyze/*/*.csv | ||
| Ancient_DNA/variant_calling/*/*.vcf.gz | ||
| Annotation/Prokka/**/*.{log,err,gbk,sqn} |
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No addition checks for gbk/sqn? These are common downstream files, so might be good to validate somehow
| QC_shortreads/fastqc/*_fastqc.{html,zip} | ||
| QC_shortreads/remove_phix/*.log | ||
| Taxonomy/CAT/**/*.log | ||
| VirusIdentification/geNomad/**/*_aggregated_classification.tsv |
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Can be removed, as you do actually check this explicitly in genomad_results
3 participants
Closes #902.
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).