fix(prepare_inputs): support relative paths
- Jun 12, 2020
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Alex Kanitz authored
# Conflicts: # .gitlab-ci.yml
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Alex Kanitz authored
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Alex Kanitz authored
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Alex Kanitz authored
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Alex Kanitz authored
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To ensure that output files for tests are identical regardless of the environment from which they are called, the script for preparing inputs now allows skipping of path expansion, essentially allowing the specification of relative file paths (e.g, relative to the location of the script).
Changes:
--no-process-paths
, which, together with setting --output-dir=""
, allows for the functionality described abovetests/test_scripts_prepare_inputs_table/test.sh
to add CLI arguments --no-process-paths
and --output-dir=""
md5
hash sums for output files created by that testprepare_inputs.py
(previousy labkey_to_snakemake.py
(accounting for the use case where the input table is not derived from LabKey); also renamed the table with information to map LabKey to Snakemake table column identifiers accordinglyFixes #120 (closed)
# Conflicts: # .gitlab-ci.yml