Closed d4straub closed 8 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 93a5869
+| ✅ 191 tests passed |+
#| ❔ 6 tests were ignored |#
!| ❗ 2 tests had warnings |!
Thanks, but somehow I cannot get nf-core tools/linting locally to work and I need to correct those failing tests ;)
Only remaining issue is
╭─ [✗] 1 Subworkflow Test Failed ──────────────────────────────────────────────╮
│ ╷ ╷ │
│ Subworkflow name │ File path │ Test message │
│╶──────────────────────────┼────────────────────────┼────────────────────────╴│
│ fasta_newick_epang_gappa │ subworkflows/nf-core/… │ Local copy of │
│ │ │ subworkflow does not │
│ │ │ match remote │
│ ╵ ╵ │
╰──────────────────────────────────────────────────────────────────────────────╯
I am a little surprised that this is an issue, will see what I can do about it.
For posterity: updating subworkflow fasta_newick_epang_gappa
was tricky because module mafft
was changed and the most recent version isnt compatible with the subworkflow:
Process
NFCORE_AMPLISEQ:AMPLISEQ:FASTA_NEWICK_EPANG_GAPPA:MAFFT
declares 6 input channels but 2 were specified
Therefore I fixed the mafft
module at version feb29be775d9e41750180539e9a3bdce801d0609
in .nf-core.yml
. That must be removed again in case the module should be updated to another version.
Template update 2.12
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).