Closed alxndrdiaz closed 1 year ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 5c7dc54
+| ✅ 115 tests passed |+
#| ❔ 25 tests were ignored |#
!| ❗ 10 tests had warnings |!
@muffato @priyanka-surana view2
branch created from formatting
branch includes all the changes required for the view
subworkflow, I tried to run the small test with two Nextflow versions (22.04.0-5697 and 22.10.1-5828) and got the following error when running theBLOBLTOOLKIT_BLOBDIR
module:
Command error:
Traceback (most recent call last):
File "/opt/conda/envs/btk_env/bin/blobtools", line 8, in <module>
sys.exit(cli())
File "/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/blobtools.py", line 105, in cli
sys.exit(subcommand())
File "/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/add.py", line 203, in cli
main(args)
File "/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/add.py", line 149, in main
parsed = field["module"].parse(
File "/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/bed.py", line 494, in parse
"name": "%s stats" % meta["name"],
KeyError: 'name'
It is possible that this error is related to the Nextflow version but I am not sure if there is anything else that could be causing the issue. Running the tests with a later version could solve the issue.
PR checklist
nf-core lint
).nextflow run . -profile test,singularity,sanger --outdir <OUTDIR>
) locally.nextflow run . -profile test_full,singularity,sanger --outdir <OUTDIR>
) locally.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).