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Export config.output_dir in MegaQC JSON #2287

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merged 8 commits into from
Feb 1, 2024
Merged

Export config.output_dir in MegaQC JSON #2287

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3a40e1c
Store output_dir as absolute path
fgvieira Jan 31, 2024
ee06735
Store cwd
fgvieira Jan 31, 2024
fea1050
Include cwd and output_dir in json
fgvieira Jan 31, 2024
dd38883
Add comments
fgvieira Jan 31, 2024
ebaa57c
[automated] Update CHANGELOG.md
multiqc-bot Jan 31, 2024
93a82a2
Revert cwd
fgvieira Feb 1, 2024
133db91
Revert
fgvieira Feb 1, 2024
649adf5
[automated] Update CHANGELOG.md
multiqc-bot Feb 1, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
- Unicode file reading errors: attempt to skip non-unicode characters ([#2275](https://github.com/MultiQC/MultiQC/pull/2275))
- Heatmap: check if value is numeric when calculating min and max ([#2276](https://github.com/MultiQC/MultiQC/pull/2276))
- Use alternative method to walk directory using pathlib ([#2277](https://github.com/MultiQC/MultiQC/pull/2277))
- Export `config.output_dir` in MegaQC JSON ([#2287](https://github.com/MultiQC/MultiQC/pull/2287))

### New modules

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2 changes: 1 addition & 1 deletion multiqc/multiqc.py
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Expand Up @@ -434,7 +434,7 @@ def run(
analysis_dir = [analysis_dir]
config.analysis_dir = analysis_dir
if outdir is not None:
config.output_dir = outdir
config.output_dir = os.path.realpath(outdir)
if use_filename_as_sample_name:
config.use_filename_as_sample_name = True
logger.info("Using log filenames for sample names")
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1 change: 1 addition & 0 deletions multiqc/utils/megaqc.py
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Expand Up @@ -49,6 +49,7 @@ def multiqc_dump_json(report):
"subtitle",
"title",
"version",
"output_dir",
],
}
for s in export_vars:
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