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Do not resolve analysis_dir to absolute path #2575

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merged 1 commit into from
May 17, 2024

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@vladsavelyev vladsavelyev commented May 17, 2024

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

fn_ignore_paths:
  - "*/work/??/??????????????????????????????" # Nextflow work directories - always same hash lengths

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 as multiqc .. 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.

@vladsavelyev vladsavelyev requested a review from ewels May 17, 2024 10:14
@vladsavelyev vladsavelyev merged commit a92b7b8 into main May 17, 2024
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@vladsavelyev vladsavelyev deleted the do-not-make-analysis-path-absoulute branch May 17, 2024 10:36
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