fix: update dry run ci for git submodule profiles

OpenOmics · Dec 12, 2023 · 01cd865 · 01cd865
1 parent ec7b5a0
commit 01cd865
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/.github/workflows/dryrun.yaml b/.github/workflows/dryrun.yaml
@@ -13,7 +13,7 @@ jobs:
     - name: Dry Run with test data
       run: |
         docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:stable /bin/bash -c \
-        "pip install -r requirements.txt;./weave run -s /opt2/.tests/illumnia_demux -o /opt2/.tests/illumnia_demux/dry_run_out --local --dry-run /opt2/.tests/illumnia_demux"
+        "source get_submods.sh; pip install -r requirements.txt;./weave run -s /opt2/.tests/illumnia_demux -o /opt2/.tests/illumnia_demux/dry_run_out --local --dry-run /opt2/.tests/illumnia_demux"
     - name: View the pipeline config file
       run: |
         echo "Generated config file for pipeline...." && cat $PWD/.tests/illumnia_demux/dry_run_out/.config/config_job_0.json

diff --git a/scripts/files.py b/scripts/files.py
@@ -157,7 +157,7 @@ def get_run_directories(runids, seq_dir=None):
         elif xml_rid and Path(run_p, f'SampleSheet_{xml_rid}.csv').exists():
             this_run_info['samplesheet'] = parse_samplesheet(Path(run_p, f'SampleSheet_{xml_rid}.csv').absolute())
         else:
-            raise FileNotFoundError(f'Run {rid}({run_p}) does not have a findable sample sheet.')
+            raise FileNotFoundError(f'Run {rid}({run_p}) does not have a find-able sample sheet.')
 
         this_run_info.update({info.tag: info.text for run in runinfo_xml.getroot() for info in run \
                              if info.text is not None and info.text.strip() not in ('\n', '')})