Closed priyanka-surana closed 1 year ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 2374c8c
+| ✅ 115 tests passed |+
#| ❔ 25 tests were ignored |#
!| ❗ 10 tests had warnings |!
Just added the definition of the hook_url
parameter as per the template
Diamond Blastp is now working 😌
LGTM. Still unable to run the small and full tests because of an unknown configuration issue, but otherwise it looks OK.
@muffato Can you run the tests?
I already ran the regular test, that's my usual way of checking PRs. I'll start the "full test" now
The full tests worked too 👍🏼
Oh, there were these warnings:
WARN: Access to undefined parameter
genomes
-- Initialise it to a default value eg.params.genomes = some_value
WARN: Found unexpected parameters:
- --diamondblastp_db: /lustre/scratch123/tol/teams/tolit/users/mm49/nextflow/src/blobtoolkit/assets/gfLaeSulp1.1.buscogenes.dmnd
- --busco_lineages_path: /lustre/scratch123/tol/resources/busco/v5/
- --ncbi_taxdump: /lustre/scratch123/tol/teams/grit/geval_pipeline/btk_databases/taxdump
- --yaml: null
- --taxa_file: null
- --taxon: Laetiporus sulphureus
- --accession: GCA_927399515.1
Oh, there were these warnings:
Yes this and a few other tidying up tasks, we will do when getting things release ready after the view subworkflow is working.
black
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black .
Once you push these changes the test should pass, and you can hide this comment :+1:
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Thanks again for your contribution!
CITATIONS.md
updated using MLA9 style..nf-core.yml
to be updated in later PR.nextflow_schema.json
– it needs updating - will do with.nf-core.yml
Tested on a clean clone and it works.