Closed atrigila closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 44f1232
+| ✅ 187 tests passed |+
#| ❔ 3 tests were ignored |#
!| ❗ 7 tests had warnings |!
Some points:
withLabel:error_ignore { errorStrategy = 'ignore' }
Thank you both for your reviews. I will address part of the issues in the nf-core module and in this pipeline.
The rationale for using the older version of checkqc was reproduce the behaviour in the internal pipeline. Now that we ensured that this module works in the nf-core pipeline, I've updated it to v4.0.3. In addition, I've changed the module design so that the even when the QC fails (due to specific QC thresholds), the output will still be written to the json report. The module now has three different test cases to account for different types of failure/success. Therefore, with this module, we do not need to have errorStrategy = ignore
. I've also updated documentation to reflect this.
Perfect, highly appreciated @atrigila 🚀
This PR adds a subworkflow and module
checkqc
for data analyzed withbcl2fastq
. In addition, it includes changes to the structure of the pipeline to support skipping this module or providing specific config files. This mode was tested with full-size test data, ascheckqc
needs complete files and file structures to perform the QC steps, otherwise the module fails.In order to avoid patching module
bcl2fastq
, a subworkflow is added to prepare the necessary directory to run checkqc so that it is not done insidebcl2fastq
.Closes #143
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).