Closed alxndrdiaz closed 1 year ago
pending tasks:
(1) Run nextflow run . -profile test_full,singularity,sanger --outdir <OUTDIR>
(2) In workflows/blobtoolkit.nf
remove ch_fasta.map { fa -> [fa[0], "${params.blobdir}"] }
and use BLOBTOOLS.out.blobdir
instead (depends on create_blobdi
r in BLOBTOOLS)
.
(3) Update docs/output.md
.
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 422c3d2
+| ✅ 127 tests passed |+
#| ❔ 15 tests were ignored |#
!| ❗ 8 tests had warnings |!
Error log from generate_summary module:
Command executed:
blobtools filter \
--summary GCA_922984935.2.subset.summary.json.gz GCA_922984935.2 \
cat <<-END_VERSIONS > versions.yml
"NFCORE_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:GENERATE_SUMMARY":
blobtoolkit-pipeline: $(blobtoolkit-pipeline --version | cut -d' ' -f2 | sed 's/v//')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
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/filter.py", line 462, in cli
main(args)
File "/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/filter.py", line 413, in main
section["title"]: section["module"].summarise(
File "/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/fasta.py", line 134, in summarise
gcs = [fields["gc"].values[i] for i in indices]
File "/opt/conda/envs/btk_env/lib/python3.9/site-packages/blobtools/lib/fasta.py", line 134, in <listcomp>
gcs = [fields["gc"].values[i] for i in indices]
AttributeError: 'bool' object has no attribute 'values'
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).