Closed kbestak closed 4 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 3a408e9
+| ✅ 211 tests passed |+
!| ❗ 1 tests had warnings |!
One additional comment. Singularity tests failed for me after the template update.
nextflow run . -profile test,singularity --outdir ./test
The error message I received was:
ERROR ~ Error executing process > 'NFCORE_MOLKART:MOLKART:MINDAGAP_DUPLICATEFINDER (mem_only)'
Caused by:
Process `NFCORE_MOLKART:MOLKART:MINDAGAP_DUPLICATEFINDER (mem_only)` terminated with an error exit status (255)
Command executed:
duplicate_finder.py \
spots.txt \
90
cat <<-END_VERSIONS > versions.yml
"NFCORE_MOLKART:MOLKART:MINDAGAP_DUPLICATEFINDER":
mindagap: $(mindagap.py test -v)
END_VERSIONS
Command exit status:
255
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
FATAL: container creation failed: image driver mount failure: image driver squashfuse_ll instance exited with error: squashfuse_ll exited: fuse: failed to open /dev/fuse: Operation not permitted
Can you check on your end whether it works on HPC @kbestak ?
To address the Mindagap Singularity issue:
This is a big one, template update 2.14 implemented, updated Mesmer, Cellpose, MultiQC, respective tests. Dev is version-bumped to 1.1.0dev Seqera container for MultiQC 1.22.1 to circumvent issue in gitpod - should this be only provided by the user? https://github.com/nf-core/molkart/issues/59 https://github.com/nf-core/molkart/issues/62 https://github.com/nf-core/molkart/issues/70
*** introduces bug that multiqc doesn't show custom qc results - neither with crops, nor quantifictions - should be fixed ASAP, but this PR is giant already.
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).