Closed muffato closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 9b1ecc3
+| ✅ 134 tests passed |+
#| ❔ 23 tests were ignored |#
!| ❗ 1 tests had warnings |!
Looks good for me.
How you picked up all the white spaces now? nf-core linting didn't complain it before?
I think it is ok to keep --busco
for busco_db and add busco_lineages
. It will be easier if we have lots of users. It is fine you have made all the changes.
I think it is ok to keep
--busco
for busco_db and addbusco_lineages
. It will be easier if we have lots of users. It is fine you have made all the changes.
Thanks for raising that. The introduction of busco_lineages
is indeed the only reason why I wanted to rename --busco
. But here are some arguments for keeping --busco
:
*_db
: --blastp
, --blastn
, --blastx
and taxdump
would remain without the _db
suffix.--busco_lineages
would like the change. --busco_lineages
is optional and the default behaviour (use all lineages that match the species) should work for many users already. These users would just use --busco
and be ok with thatI decided to remove the commit that renamed the parameter
This is a bit of cleanup of the code and parameters that I want to get in before #97 and finally reaching v1.0.0. The Changelog mentions a tentative intermediate v0.5.0 release, though I'm not sure it will happen at all. If I can get all the work done to support draft assemblies soon enough, I may ship both as v1.0.0.
I've removed all the
--blast*
parameters because end users could not change them without breaking the pipeline.I've renamed
--busco
to prepare the introduction of the--busco_lineages
parameter in #97 .I've removed
--taxa_file
because it didn't add anything more than--taxon
.I've fixed the channel factories so that they're correctly queue/value channels, and paths are properly constructed as paths (files).
Whitespace cleanup
And two pipeline changes:
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).