Do not resolve analysis_dir to absolute path #2575
Merged
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Address #2569
Context:
Nextflow working directories are ignored by default when performing the log file search: https://github.com/MultiQC/MultiQC/blob/main/multiqc/config_defaults.yaml#L124
The use case for that is when MultiQC runs outside of a nextflow workflow, and you want to pick the workflow outputs, but not the intermediate working files.
However, you still want to make sure MultiQC works while executed inside a nextflow workflow as a job. The standard use of MultiQC inside Nextlfow is to change into the working directory (e.g.
cd /work/d3/65b98a3d9c7f67b7f3a2f2b48b5a59
, then run asmultiqc .
. It worked up until v1.22 because previously MultiQDC didn't expand the.
path, so the directory name didn't match the exclusion pattern. v1.22, however, expands input paths to absolute, so the directory name matches the exclusion pattern and gets ignored.I'm reverting to the v1.21 behavior and keeping relative paths.