From 0cb8f1a8524ca71526d99e863f3743c79cdbcbae Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@unibas.ch>
Date: Fri, 12 Jun 2020 13:05:54 +0200
Subject: [PATCH] rename
---
README.md | 2 +-
...uts.labkey_to_snakemake.dict.tsv => prepare_inputs.dict.tsv} | 0
scripts/prepare_inputs.py | 2 +-
tests/test_scripts_prepare_inputs_labkey/test.sh | 2 +-
tests/test_scripts_prepare_inputs_table/test.sh | 2 +-
5 files changed, 4 insertions(+), 4 deletions(-)
rename scripts/{prepare_inputs.labkey_to_snakemake.dict.tsv => prepare_inputs.dict.tsv} (100%)
diff --git a/README.md b/README.md
index 6c76bbc..c8dca57 100644
--- a/README.md
+++ b/README.md
@@ -257,7 +257,7 @@ help screen with option '--help' for further options and information):
python scripts/prepare_inputs.py \
--labkey-domain="my.labkey.service.io"
--labkey-domain="/my/project/path"
- --input-to-output-mapping="scripts/prepare_inputs.labkey_to_snakemake.dict.tsv" \
+ --input-to-output-mapping="scripts/prepare_inputs.dict.tsv" \
--resources-dir="/path/to/my/genome/resources" \
--output-table="config/my_run/samples.tsv" \
--config_file="config/my_run/config.yaml" \
diff --git a/scripts/prepare_inputs.labkey_to_snakemake.dict.tsv b/scripts/prepare_inputs.dict.tsv
similarity index 100%
rename from scripts/prepare_inputs.labkey_to_snakemake.dict.tsv
rename to scripts/prepare_inputs.dict.tsv
diff --git a/scripts/prepare_inputs.py b/scripts/prepare_inputs.py
index 4ac90ab..1efc031 100755
--- a/scripts/prepare_inputs.py
+++ b/scripts/prepare_inputs.py
@@ -61,7 +61,7 @@ def parse_cli_args() -> argparse.Namespace:
type=argparse.FileType('r'),
default=os.path.join(
os.path.dirname(__file__),
- 'prepare_inputs.labkey_to_snakemake.dict.tsv',
+ 'prepare_inputs.dict.tsv',
),
help="lookup table with mappings from input (LabKey or LabKey-like) "
"to output (Snakemake) table; default: '%(default)s'",
diff --git a/tests/test_scripts_prepare_inputs_labkey/test.sh b/tests/test_scripts_prepare_inputs_labkey/test.sh
index 45aea36..3f8b721 100755
--- a/tests/test_scripts_prepare_inputs_labkey/test.sh
+++ b/tests/test_scripts_prepare_inputs_labkey/test.sh
@@ -33,7 +33,7 @@ EOF
python "../../scripts/prepare_inputs.py" \
--labkey-domain="${LABKEY_HOST}" \
--labkey-path="/Zavolan Group/TEST_LABKEY" \
- --input-to-output-mapping="../../scripts/prepare_inputs.labkey_to_snakemake.dict.tsv" \
+ --input-to-output-mapping="../../scripts/prepare_inputs.dict.tsv" \
--resources-dir="../input_files" \
--output-table="samples.tsv" \
--config-file="config.yaml" \
diff --git a/tests/test_scripts_prepare_inputs_table/test.sh b/tests/test_scripts_prepare_inputs_table/test.sh
index e9bc935..ebd9391 100755
--- a/tests/test_scripts_prepare_inputs_table/test.sh
+++ b/tests/test_scripts_prepare_inputs_table/test.sh
@@ -22,7 +22,7 @@ cd $script_dir/
# Run tests
python "../../scripts/prepare_inputs.py" \
- --input-to-output-mapping="../../scripts/prepare_inputs.labkey_to_snakemake.dict.tsv" \
+ --input-to-output-mapping="../../scripts/prepare_inputs.dict.tsv" \
--resources-dir="../input_files" \
--output-table="samples.tsv" \
--config-file="config.yaml" \
--
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