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Broaden anglerfish run search #304

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merged 1 commit into from
Jan 30, 2024
Merged

Broaden anglerfish run search #304

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4 changes: 4 additions & 0 deletions VERSIONLOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
# Scilifelab_epps Version Log

## 20240126.1

Discover latest anglerfish run even if embedded in subdir of run dir

## 20240122.1

Enable copy_field_art2samp to copy values from Aggregate QC steps
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2 changes: 1 addition & 1 deletion scripts/parse_anglerfish_results.py
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Expand Up @@ -35,7 +35,7 @@ def find_latest_flowcell_run(currentStep: Process) -> str:


def find_latest_anglerfish_run(latest_flowcell_run_path: str) -> str:
anglerfish_query = f"{latest_flowcell_run_path}/*anglerfish_run*"
anglerfish_query = f"{latest_flowcell_run_path}/**/anglerfish_run*"
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I belive the double asterisk is sort of a special feature of some shells, have you tested this on the LIMS server?

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Tried it now

In [6]: p="repos/**/scripts"

In [7]: from glob import glob

In [8]: pwd
Out[8]: '/opt/gls/clarity/users/glsai'

In [9]: glob(p)
Out[9]: ['repos/scilifelab_epps/scripts']

Seems to work :)

anglerfish_glob = glob.glob(anglerfish_query)

assert (
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