Closed muffato closed 11 months ago
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nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit f06f8cf
+| ✅ 132 tests passed |+
#| ❔ 20 tests were ignored |#
!| ❗ 1 tests had warnings |!
In TOLSD-1312 three species failed because their JSON file didn't have an assembly record. This seems to be a transient error as further runs of
ncbi datasets
produced a complete JSON.However, the pipeline didn't behave optimally as it considered the DATASETS process to succeed and it's only later, in the CREATE_TABLE process, that an error was raised. At this point, we can't use "resume" because it would only try CREATE_TABLE again and again.
In this PR, I propose to check the validity of the JSON file right after running the
datasets
command, so that if the JSON file doesn't have any report, the process will fail immediately, and "resume" will restart it.cc @cibinsb
PR checklist
nf-core lint
).nextflow run . -profile 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).