Closed alxndrdiaz closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 0d7ed76
+| ✅ 176 tests passed |+
#| ❔ 1 tests were ignored |#
!| ❗ 21 tests had warnings |!
When running nextflow run . -profile test --outdir=/home/nf-core/tests,
the following error is raised:
Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CREATETAXDB:CREATETAXDB:KAIJU_MKFMI (database)'
Caused by:
Process `NFCORE_CREATETAXDB:CREATETAXDB:KAIJU_MKFMI (database)` terminated with an error exit status (127)
Command executed:
kaiju-mkbwt \
\
-n 2 \
-o database \
database.faa
kaiju-mkfmi database
cat <<-END_VERSIONS > versions.yml
"NFCORE_CREATETAXDB:CREATETAXDB:KAIJU_MKFMI":
kaiju: $(echo $( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
END_VERSIONS
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 4: kaiju-mkbwt: command not found
Should all nf-test related bugs should be fixed before merging this branch?
Is that because you're missing singularity/conda or docker in your command ?
Is that because you're missing singularity/conda or docker in your command ?
I confirm this was the issue, locally the test is successful, using: nextflow run . -profile test,docker --outdir=/home/nf-core/tests
:
executor > local (12)
[d4/4e3f34] process > NFCORE_CREATETAXDB:CREATETAXDB:GUNZIP_DNA (haemophilus_influenzae.fna.gz) [100%] 1 of 1 ✔
[37/3571b3] process > NFCORE_CREATETAXDB:CREATETAXDB:CAT_CAT_DNA (database) [100%] 1 of 1 ✔
[f4/67a5d8] process > NFCORE_CREATETAXDB:CREATETAXDB:PIGZ_COMPRESS_AA (database) [100%] 1 of 1 ✔
[18/1e4589] process > NFCORE_CREATETAXDB:CREATETAXDB:CAT_CAT_AA (database) [100%] 1 of 1 ✔
[f9/3a8697] process > NFCORE_CREATETAXDB:CREATETAXDB:CENTRIFUGE_BUILD (database) [100%] 1 of 1 ✔
[46/be5c7e] process > NFCORE_CREATETAXDB:CREATETAXDB:DIAMOND_MAKEDB (database) [100%] 1 of 1 ✔
[5c/f5a2d0] process > NFCORE_CREATETAXDB:CREATETAXDB:KAIJU_MKFMI (database) [100%] 1 of 1 ✔
[ac/c4ba22] process > NFCORE_CREATETAXDB:CREATETAXDB:FASTA_BUILD_ADD_KRAKEN2_BRACKEN:KRAKEN2_ADD (database) [100%] 1 of 1 ✔
[d5/5549eb] process > NFCORE_CREATETAXDB:CREATETAXDB:FASTA_BUILD_ADD_KRAKEN2_BRACKEN:KRAKEN2_BUILD (database) [100%] 1 of 1 ✔
[0d/b54c3c] process > NFCORE_CREATETAXDB:CREATETAXDB:UNZIP (megan-nucl-Feb2022.db.zip) [100%] 1 of 1 ✔
[17/52f9c1] process > NFCORE_CREATETAXDB:CREATETAXDB:MALT_BUILD (1) [100%] 1 of 1 ✔
[5a/18e49e] process > NFCORE_CREATETAXDB:CREATETAXDB:MULTIQC [100%] 1 of 1 ✔
-[nf-core/createtaxdb] Pipeline completed successfully-
Completed at: 21-May-2024 10:25:38
Duration : 2m 24s
CPU hours : (a few seconds)
Succeeded : 12
Error related to failed check (nf-core CI / nf-test ...):
Found 1 files in test directory.
Test pipeline: NFCORE_CREATETAXDB
java.lang.RuntimeException: Path /home/runner/work/createtaxdb/createtaxdb/.nf-test/tests/aa06ef15b1d2bac6ab77b23519901408/output/kraken2/db/hash.k2d not found.
Test [aa06ef15] 'test_profile' FAILED (128.576s)
Assertion failed:
1 of 6 assertions failed
Nextflow stdout:
Nextflow stderr:
FAILURE: Executed 1 tests in 128.581s (1 failed)
Error: Process completed with exit code 1.
OK I will investigate!
@alxndrdiaz I went full whack as I got annoyed at the other PR I'm working on 😆
But thanks for putting the foundations in!
Even if it sounds a bit weird, could you 'review' your own PR to check my changes are OK?
I used here: https://hackmd.io/psKX3BvyRZepqZmV1VjvpA as my checklist
Note that there is no metromap yet, not usage docs (I will do this at the end prior release)
@jfy133 After a (very fast) review I confirm all changes were made as described in the checklist. Also all three tests (with docker, singularity and conda) work as expected [Nextflow 24.04.1, nf-core/tools 2.13.1]. There is only a warning that is raised when running any of the tests (it seems it does not affect the results):
WARN: Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value
Also the conda test raises a warning which does not affect the results as well:
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
There is a problem with your Conda configuration!
You will need to set-up the conda-forge and bioconda channels correctly.
Please refer to https://bioconda.github.io/
The observed channel order is
[bioconda, defaults, conda-forge]
but the following channel order is required:
[conda-forge, bioconda, defaults]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Thanks for the notes on the two warnings!
The conda one generally isn't important. The monochrome log thing is from the template and will fix that in a different PR.
Thanks for the review of my half of the PR! Will merge now
PR checklist
nf-core lint
).nf-test test main.nf.test -profile test,docker
).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).Fixes #1