From 01cd8655ce401540b08e08e4fc8e01c59f0b7aca Mon Sep 17 00:00:00 2001 From: Ryan Routsong Date: Tue, 12 Dec 2023 11:11:42 -0700 Subject: [PATCH] fix: update dry run ci for git submodule profiles --- .github/workflows/dryrun.yaml | 2 +- scripts/files.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/dryrun.yaml b/.github/workflows/dryrun.yaml index ae8709a..c9b64de 100644 --- 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 index 479602b..9ae6994 100644 --- 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', '')})